No Nintendo PC port is complete without people autistically screeching about ceases and desistisesses. Worst case, I think the developer can play around with the assets and turn Link's Awakening into something more legally distinct. Perhaps swap the characters with ones from Arthurian legend, while keeping most of the map design and story intact. Just a thought I suppose.
Either that or simply ask for players to supply their own Link's Awakening roms, which is what other PC ports do and why they cannot be taken down.