Rex, I've never seen or heard of that happening before. My thought was that, like others have said, perhaps somebody sat on the top of the sport bar or repaired body work is now deteriorating? I'm not an expert but I've been on these boards a long time and never saw that happen so I waited to see others commment.
My '94 developed a hairline crack on the hood (above the passenger side vent) 6 months after I bought it in '96. somewhat common problem on the '94's. Got it replaced under warranty as couple of dealers, particulary Eddie Martin (the great viper Tech at Bill Luke dodge in Phoenix) told me if you try and fix it it will eventually crack again due to the composites used in the hood. Seems like the sport cap is the same material. I worked at chrysler financial at the time and the zone service director really didn't want to pay the $14K warranty claim but he knew that was the only way to fix it correctly so he authorized it.
The motor mounts eventually fail on all vipers, don't think that had anything to do with your stress cracks. Used sports caps can be found, you might need to replace yours vs. fix it? good luck, Mike