1) I don't know how compatible PCMCIA slots are, but if it fits, it should work. It would probably show as a removable media reader, though.
2) every modern Amiga CD file system should be able to read Joliet.
Every useful burning program should be able to write ISO9660 level 2, not only early versions.
As you've got WinUAE up and running you could as well use an Amiga program to burn Amiga CDs, for example MakeCD. Enable uaescsi option on Expansion panel.
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