For libraries, you can achieve something close enough by using the old way to mix 68k and PPC files on one single volume:
your.library <- 68k or alien code
your.library.elf <- MorphOS code

On MorphOS, the ".elf" file will be used. The other one on other systems.

Or just use an IconX script using "version MorphOS" to run a binary or another.
The end user will only see one directory containing one single icon...