It was funny in Hitman, but I think that in part that was because Ennis had to write a book that took place in the regular DCU instead of the relative freedom of Vertigo, so it was mostly implied, and Bueno Excellente came across as the dirty old man of countless mid-20c jokes and cartoons. (There's a partly-hidden newspaper headline in Section 8's last appearance that implies that, yes, Bueno's "perversity" does involve buggery, but it's not stated outright.)
But he keeps going back to it, again and again and again. Aside from the example mentioned above, and something similar in the Hitman/Lobo special, there are multiple incidences in Preacher (Herr Star in San Francisco, Jesus de Sade, once in Salvation), in his Hellblazer run (a male prostitute when Constantine was a homeless drunk and the "fuckpig" demon in Son of Man, maybe the worst thing that Ennis has ever written), at least once in Punisher (Soap), and a couple of times so far in The Boys (Tek Knight was pretty much defined by it, and also it's implied that Black Noir did it to Hughie in Herogasm.) And also in Crossed, at least once; I gave it up after the first issue. That's just off the top of my head. It's not like no one else mentions it; Alan Moore has used male-on-male rape at least a couple of times (one of the most horrific scenes that I've seen in comics was the rape of Johnny Bates in Miracleman, and not too far behind it was the Invisible Man's death at the hands (and other organs) of Hyde in LoEG), but not with that odd fascination-with-a-thin-veneer-of-hilarity that Ennis has.
To paraphrase that old joke about the bear hunter, I don't think that Ennis keeps coming back to it for the hunting.