I know that UAE is a pretty good Amiga Emulator, but it seems aimed to emulatr an Amiga 500 or a 1200. While the CD32 is similar to the Amiga 1200 - 68EC020 CPU, 2 MB ChipRAM, AGA - it has a special Chip, the Akiko, which does not seem to be supported by UAE.
Amiga Forever lists CD32 Support, but it is not stated if that just means supplying the KickStart ROMs or if it actually includes Akiko Emulation. As it's commercial, I can't just try it out before.
Also, there is Airsoft's Akiko, which was last updated in 2002. Sure, there is always a point where one is "done" writing an emulator, but I still wonder if this is any good and even compatible with newer systems? It looks also only his UAE Modifications are Open Source, while the Akiko-part is not part of that.