Amiga, Inc. has the "Amiga" trademark, but do they have the "AmigaOS4.1" trademark?
They dont have to. You can not register "AmigaOS" trademark (if not already registered) because it contains word Amiga which is registered trademark of Amiga, Inc. and their trademark is used for similar stuff.
Hyperion Entertainment could maybe get away by using AOS acronym. There is already ACube which stands for Amiga Cube but officially there is only "ACube".
Can Hyperion successfully argue that it's not a derivative work?
That would be cool ;-)