the amount of strength you lose depends on where you're cutting it and how much you cut it. in the wheel well if you cut past the pinch seam you'll lose a lot of strength, but i'm pretty sure it can be welded back together. also, if you cut the rear quarter panel, there ends up being a gap between the outwe sheet metal and the pastic on the sides of the trunk space. i had my rear's trimmed for bushwackers but didnt go past the pinch seam, but trimmed the rear quarters a lot. it's possible to weld a piece of metal to close off the gap, but i haven't yet. the only thing i notice since the bushwackers and rear quarter panel trimming is a LOT MORE road noise and some squeaking from the area. but my XJ's a tank, so it just adds to the effect.
hope that made some sense