The Ultra models (and any version running EOS 4.x I believe) can load and save wav files to and from a DOS formatted floppy disk. I have never tried this with a DOS formatted Syquest or zip disk though this may well work too.
A floppy disk limits you to 1.4 Mb.
You can, of course, transfer wav files of any size (up to the RAM maximum) to and from the sampler over SCSI. A much better solution but a whole different set of hurdles.
In terms of sound libraires I would have to disagree on the size issue. Emu were in the sampler business some time before Akai and my understading is that they have the biggest sample library there is (also worth remembering that this library also includes every sound released in every EMU PCM synth).
However, the units certainly will load Akai disks so the debate is not that relevent.
As to the quality. Well thats always subjective. I have a whole bunch of EMU CD_ROMs that came with my Ultra and several more I bought for my ESI032 (orbit, planet phat etc.). These are all high quality but I make trance/techno and sample quality is not important.
Most great sounds involve the use of effects as well as the raw sound. None of the banks UI have loaded into the Ultra use effects and you have to apply them yourself (which is fine by me). It would be unfair to compare these raw sounds to the processed sounds you get out of something like the JV2080.