I think they released singles in small disks because they had less songs, so required less space... then they just stopped, maybe because they wanted to add remixes? Though even singles with very few tracks still have the same disk size as an album... maybe they just thought it was more practical to have all CDs be the same size~ I think that's the best I can do to explain what a 8cm single is...
The biggest difference between Ayu's 8cm and re-release singles, though, is probably the rarity
They're really hot collector's items because they're out of print~