My interpretation is that Poorgrass gets a ha’penny bonus if the pig-killing is a ‘bad one’.
Hardy is known to have been opposed to the prevalence of inhumane pig slaughter and in particular the practice of slow-bleeding. We can see this represented in Jude’s revulsion at the cruelty of Arabella’s preferred methods in Jude the Obscure.
In ‘Food in the Novels of Thomas Hardy: Production and Consumption’
By Kim Salmons, the author states
In Harry’s personal notebooks, he records a letter of August 1919 that he sent to Mr. W. J. Malden, Chair of the Wessex Saddleback Pig Society, in which he remarks that he is ‘more bent on human methods of slaughter that [sic] on anything else in relation to it.’ Hardy continues the letter with a suggestion: ‘I am not aware if the stupid custom still prevails of having pork “well bled”. This impoverishment of the meat for the sake of a temporary appearance should, I feel, be discouraged by the Society’. At the bottom of the letter in Hardy’s notebook, he remarks in the third person, ‘It is satisfactory to know that Hardy’s suggestions were acted upon by the society’. (Taylor 1979, p. 270).
Salmons goes on to note that Hardy had hoped the slaughter scene in Jude would
serve a humane end in showing people the cruelty that goes on unheeded under the barbarous regime we call civilisation.
So I would read it that Poorgrass gets a little extra compensation if the pig kicks up extra fuss about being killed slowly. The 9/9 was his regular wage covering all of his duties, including pig-killing, but as pig-killings happen only infrequently any bonus related to a difficult one seemed worthy of special mention.