UAE is an emulator. No doubt to "emulate" the floppy drive it has to emulate many other parts too which in turn slow-down the Amiga. You cannot simply replace a part of the hardware with software running ON the hardware.
A hardware plug-in replacement for the floppy drive however is self contained. The Amiga merely sees a floppy drive so it runs just the same as if it was a REAL floppy drive, possibly faster for software which doesn't rely on strict read timings.
