I believe the writers had the credo of "O'Brien must suffer."

Like, literally. Posted in the writing room, along with the blindfolded bust of Gene Roddenberry

Although I still think my favorite "torture O'Brien" moment is in the Rascals episode of TNG, when he's trying to deal with bb!Keiko

I recently rewatched the DS9 episode "Hard Time" and jesus tap dancing christ the writers have it out for him