def. dont drill holes if the floor joists are only 2x8's. If they were 2x12's, you could drill a 1 or 1.5" hole about 1/3 of the way up the joist with no problem.

you could always bolt a 2x12, like 24" long or so, to each side of 2 joists that were 3'-4' apart, then drill the holes in the four 2x12s and slide a pipe through. That would make a pretty easy set up without fucking up your structure.