I think they care mostly about which of their IP's are still making them revenue. When they cancelled CTR, I'm sure there was talk of releasing Chrono Trigger for DS down the line. As for ROM hacks, I'm sure they got C&D'd due to the sheer illegality.
I'm sure if it's a simple fangame which is, based on your post in gfx section, using custom/edited sprites and not direct rips, I don't think you'll need to worry about getting that dreaded email.