Bill Ferny flinched and shuffled to the gate and unlocked it. ‘Give me the key!’ said Merry. But the ruffian flung it at his head and then darted out into the darkness. As he passed the ponies one of them let fly with his heels and just caught him as he ran. He went off with a yelp into the night and was never heard of again.
‘Neat work, Bill,’ said Sam, meaning the pony.
(RK 6.viii.999)
Given Sam's love for the pony and loathing of Ferny, it's hard to see why Sam would have given it the name of a villain who had cruelly mistreated it. As a joke? Perhaps, but to me at least that doesn't seem a joke Sam was likely to make. It would seem hurtful to Bill and too good for Ferny. I just don't see it as in his character. Contrast this with the humor we hear of in The Grey Havens, where we learn that the renewed Bagshot Row came to be known as Sharkey's End, a 'purely Bywater joke' for the place where the Saruman met his end (RK 6.ix.1021-22). But Sam was not from Bywater and Saruman was hated. The bitterness of the joke was founded on a very real sense of Saruman's deserts.
Now to be honest I can only admit that my incredulity proves nothing. It's not much of an argument. Yet who else could Bill the pony be named after? Is there any other alternative? There is, though I concede it's not the strongest or most direct. I just like it better.
What if Bill the pony is named after Bilbo? After all Sam loved the old hobbit, whom he met again in Rivendell after many years, and as far as we can tell it was in Rivendell that Sam first began using the name for the pony. It is there in any event that our attention is drawn to this fact. The text, moreover, supplies us with a parallel for a hobbit naming a pony after a beloved friend. In Minas Tirith Frodo gets a pony which he will ride all the way home. He named the pony 'Strider' and the only time its name is mentioned is in conjunction with Bill (RK 6.ix.1027):
On September the twenty-first they set out together, Frodo on the pony that had borne him all the way from Minas Tirith, and was now called Strider; and Sam on his beloved Bill.