If I was doing it, I'd personally want to open the empeg and put some foam cushioning in at the back of the unit to ensure the drive tray couldn't hit the back of the case sharply.

It'd void the warranty, and I'm not sure what the effects would be on drive life from running them in a strange orientation, but ensuring the drive won't hit anything solid from large vertical shocks (potholes, etc) would be a good move.

Hugo