Are you planning on using the AEBS AirDisk as a Time Machine volume? If so, to my knowledge, Apple does not support such usage (although people have unofficially been able to skirt around it by first plugging in the device locally, setting it as the Time Machine volume, disconnecting it before [or after] backing up, and then reattaching it to the AEBS).
Other than that, I'd imagine any differences in speed, other than those related to the hard drives themselves, would be negligible--but I've never tried.