How odd, Nestopia actually searches for the blackest color in its palette and uses that. Should be trivial to change it to use palette entry 0. The function is GetBlack() in NstVideoFilterNtsc.cpp line 120, which ultimately sets as used in BlitType() on line 142. I'm not familiar enough to know where it can get access to NES palette RAM, though (the palette it has a reference to looks to be an RGB version of the full NES palette, rather than palette RAM).