The UAE family has been updated to support using .scp image files now! This means that every type of disk protection can now be used with the emulation. Just select the .scp image file (or archived as .zip, .7z, etc.) in the floppy drive selection and away you go. The disk loads just like the original, with full copy protection intact.
Thanks to Keir Frazer for creating the code for E-UAE and FS-UAE, and Toni Wilen for merging it to WinUAE.
.scp images are generated by SuperCard Pro hardware. For more info see:
http://www.cbmstuff.com/proddetail.php?prod=SCP