It's the same sort of situation as with any emulator that uses the original ROM files from the orginal machine....
ROM is still software, and hence it's still copyrighted. This is one of the major problems wiuth the Amiga emulation scene. In theory, you can't run an emulator if you don't own the original machine.
As it stands, I dont think many companies will mind you emulating a machine that isn't manufactured anymore. In fact, some actively encourage it by making the ROMs public domain (bad example, but the Sam Coupe emulator for the PC now has public domain ROMs, and the Spectrum ROMs have been made public domain by Amstrad I believe).