Both parts of the phrase here are used in their dictionary meaning, but in a sarcastically sadistic manner, as with many things with Bonhart.
"To take pains" means to try very hard. One would think Bonhart was referring to having to cut the group's heads off and whatnot, but it's hardly a lot of work for him - he had just killed them all very easily, while everyone else the group had attacked prior to that point couldn't.
Hence, Bonhart isn't referring to the physical effort necessary to decapitate them, but to the nuisance of having to do so. He's done the crux of his job, which was to kill them and capture Ciri (although he was supposed to kill her as well), but now he's got to go to the trouble of doing this, just to prove to the person who commissioned him that he's done the deed.
As for "go off", it's once again the dictionary meaning, in this case "to spoil", e.g. when speaking of food. This is mainly where the sadistic part kicks in.
Bonhart has captured Ciri. He wasn't supposed to, but he did, with his own twisted agenda in mind. He disabled her physically, and now he's working to cripple her emotionally in order to prevent her from rebelling against him.
He's just killed her friends in cold blood, and she had to watch while he did some of it. Then she failed to avenge them, when she attacked Bonhart and he dispatched her very easily as well, and with what - a single blow to the head with his hand. She even remarks in her inner monologue that he's bested her as if she was an incompetent little girl.
Now on top of that, he's decapitating her friends' dead bodies. He doesn't need to do that - at this point, by capturing Ciri instead of killing her he's already breached his contract. He's doing this purely to further hurt Ciri emotionally, which is why he has her forcibly watch the whole thing.
Cutting their heads off solidifies their status as dead. Think of heads displayed on spikes - this is the same logic. However, he goes one step further: he's going to dehumanise them, by reducing their last remains to "goods", as if they weren't humans but some common commodity to him, and to something perishable, so that they evoke not only thoughts of death and mortality, but also of decomposition and rot, which is a big turn-off for most people.
And he doesn't even have to do that either! When the people who hired him visit him earlier and later it's clear that they're not somewhere too far away. Even if they are, showing the group's dead bodies would be much easier than cutting their heads off to preserve them.
He goes to all this "trouble" simply to show off to Ciri what a sadist he is, and he does so in a manner most disrespectful of her comrades.
