It depends on the type of flat roofing system you have. If you have a metal or asphalt (modified bitumen or built-up) roofing system, the answer is probably no. If you have a single-ply membrane (EPDM, TPO, or PVC) roof, a cat could damage it with repeated claw sharpening. And you might just want to leave them alone. Cats can be a good deterent for birds which tend to be even more problematic.
Here's something else to consider.
Birds damage flat roofs more than any animal I know of. Perhaps there’s a good reason to keep a hungry cat on a commercial flat roofing system—they might be a good bird deterrent.