It's worth a try ... however, it does not sound as efficient. The entire configuration was designed to maximize convection, i.e. the hottest components located near the top to draw cool air up. Forcing air down through the Mac would actually send hot air down into the case.
As for the reverse airflow through the FDD, that would not eliminate dust build-up. In fact more dust might be drawn in from the top than gets sucked in from the bottom. Either way, without a dust shield, the FDD is going to get filled up with dust bunnies no matter which way the air flows. Apple finally added a slot cover to the Superdrive around the Colour Classic era to prevent dust from getting sucked-in through the drive. These drives were almost fully enclosed as well.