Both my 99 and 93 Troopers had rear links that had a bit of a bend from the factory, though not as much as the Stinkyfab ones. Sometimes people freak out when they notice that bend, thinking there is something wrong. But I have heard that others were straight from the factory, so I don't know what you guys got.
Having said that, I think upgraded links are a good idea if you are going off-road with any seriousness...I saw what Desha did to the link on her old RS Trooper in Moab a few years back, pretzelized is a word that comes to mind.
I have Indy4x straight links on my Trooper, and it is apparent from the missing paint on the underside that they contact the rocks fairly often. Hit a factory link hard enough and it could fold up on you easily.
While bent links would offer a little more clearance, straight ones are going to be stronger and I'm not sure the clearance is worth getting the bent ones.