Dictionary definition of Epilepsy:
A neurological disorder marked by sudden recurrent episodes of sensory disturbance, loss of consciousness, or convulsions, associated with abnormal electrical activity in the brain.
Let's have a look at Simon:
[...] the choir huddled into line and stood there swaying in the sun [...]
one of the boys flopped on his face in the sand and the line broke up. // Simon is particularly delicate. Victims of epilepsy are more likely to faint as a result of over-heating.
"He's always throwing a faint", said Merridew. "He did in Gib.; and Addis; and at matins over the precentor." // Epileptic victims are more likely to faint in stressful situations, such as performing in a choir, or as a result of tiredness. Modern-day causes of epilepsy involve taking drugs, which similarly degrade your body's functionality. Note 'recurrent episodes' in the definition, and that Simon is 'always throwing a faint'.
Now that the pallor of his faint was over, Simon was a skinny, vivid little boy, with a glance coming up from under a hut of straight hair that hung down, black and course. // Epilepsy is characterised by its suddenness. Similarly, Simon's fits seem to turn on and off at the flick of a switch.
For a moment or two Simon was happy to be accepted and then he ceased to think about himself. When he bashed into a tree Ralph looked sideways and Robert sniggered. Simon reeled and a white spot on his forehead turned read and trickled. // Epileptic victims suffer from sensory disturbance, making Simon more likely to get distracted from something as small as the fact that Ralph 'smiled constrainedly' at him. The fact that he is 'reeling' even though he has 'allowed his pace to slacken until he was walking', hints that he gets dizzy easily, which is something that causes epileptic attacks and so is a common attribute of epileptic victims.
Simon lowered his head, carefully keeping his eyes shut, then sheltered them with his hand. // It's well known that epileptic victims are prone to seizures/fainting as a result of abnormal electrical activity triggered in the brain because of flashing light. Simon was experiencing something similar beneath a veil of leaves. Sunlight spread across a forest canopy will cause a 'dappled' effect of irregular light/dark patterns which are associated with with flashing lights. This would have been heightened by swaying branches and Simon's movement underfoot.
[...] the Lord of the Flies hung on his stick and grinned. [...] In Simon's right temple, a pulse began to beat on the brain. // That about says it all. Normal victims of fainting don't hallucinate like this. Golding may well have known about the correlation between religious experience and epilepsy. Simon is probably a christ-like figure. It is more likely that the pig-lord Simon saw was an epiphany about human nature, than a convenient figment of his stressed-out imagination.
Yet the way we refer to an event is lot more telling than the details of the event itself. Crucially, Golding did not say Simon 'felt rather faint so he soon passed out'. If he had, that would imply that he viewed it as an isolated, random, and unexpected event that anyone could experience. Instead, Golding explains that Simon 'knew that one of his times was coming on'. Therefore, Simon's continual fainting is more likely to be a diagnosed condition of which he is fully aware, such as epilepsy.
It's also worth noting that the boys may lack sleep. Sleep deprivation, if Simon has it, is something that would make him more likely to have epileptic attacks.
Although Ralph is the only boy who helps Simon with the shelters, he describes them as 'tottery'. So the boys rest in 'tottery' shelters on a deserted island, but have up to this point enjoyed living in a first-world country where even Piggy had a warm bed. It's like camping night after night without a sleeping bag, for someone who has never gone camping before.
In addition, Simon has the burden of moral conscience - he alone voices the littluns' fears of the 'beastie', saying 'maybe it's only us'/'what's the dirtiest thing there is?', but when the boys laugh in his face they make it clear that Simon is alone in his traumatic fear. Simon is probably no older than ten, given that he is so short (see below) and Piggy calls him 'young Simon'. From all this, are we supposed to gather that Simon is sleep-deprived?
Simon, walking in front of Ralph, felt a flicker of incredulity - a beast with claws that scratched, that sat on the mountain-top, that left no tracks and yet was not fast enough to catch Samneric.
Simon does not believe, like Jack, that the beast is something that they can hunt and kill. He is too mature for that: 'his eyes were dim with the infinite cynicism of adult life'. His free indirect speech shows that he thinks of the beast as the people, something they can't control. If had to lose sleep as a pre-teen kid, it would be over an indestructible evil residing inside us ("my" belief), rather than a freak bogeyman on the top of a mountain (everyone else's belief).
However Simon thought of the beast, there rose before his inward sight a picture that was at once heroic and sick.
Apart from evidence to suggests Simon is epileptic, Golding had incentive to give him epilepsy in the first place.
Simon is a genius. In spite of his youth, he has incredible perception that Golding believed no-one of the time actually possessed. But his unique insight - that the 'beastie' lies in the people - helps make him an outsider. He is indeed epileptic. In the context of a barbaric society, epilepsy is not just a medical condition but a weakness.
Epilepsy is a tool that makes him more delicate, easier to victimise, and thus even more of an outsider. (Not because epilepsy makes him frail, but because people who are more frail are more likely to have epilepsy). This drawback makes it more believable that he could be killed, and didn't manage to flee/put up any fight. If he had optimal physical ability, no-one would buy it.
His epileptic attacks no doubt take their toll on both his energy and the minimal respect that people have for to him. All the while, this effect contributes to Golding's theme of outsiders (see below), relating to the wartime prosecution that made him believe "man produces evil as a bee produces honey", which is the whole point of the book.
Simon is described as 'skinny', and Ralph's language implies that he is short -
"If Simon walks in the middle of us", said Ralph, "then we could talk over his head."
Not to mention the fact that he can hardly keep up -
The three of them fell into step. This meant that every now and then Simon had to do a double shuffle to catch up with the others.
Golding's revulsion of Nazism was less than a decade old when he wrote the novel, so survival of the fittest and the rejection of outsiders is a recurring theme. The theme of outsiders is important, making Simon's epilepsy important too. Much like the child with the birthmark who was burned in wildfire, the democratic leader who was hunted down, and the overweight geek who was knocked off a cliff, Simon (ironically mistaken for 'beastie') was murdered by savages.
Ralph says to Simon in chapter 7 'you're batty' and to Jack that 'He's queer. He's funny', and Piggy also dismisses him: 'he's cracked'. Simon is also too kind for his own good: he gives Piggy his share of the meat, thereby vexing Jack at his worst. He advises Jack to suck his wound despite having been bullied by him. He selflessly picks food for the littluns. He helps Ralph carry Percival to the shelter, remains loyal to him, and works consistently hard on the shelters (despite Ralph's taunts).
Simon's 'goodness' goes hand-in-hand with his earlier drawback, epilepsy, as they both portray him as a pushover (easier to kill). Given how convenient it would have been for Golding to give Simon epilepsy, and all the evidence that backs it up, I believe that Simon is epileptic.