Thanks for your effort on this. I'm a little surprised that the nes core like nestopia can't handle hq2x. Maybe that algorithm is too complex. It'd be cool to get any scalers working for better sharpness. For example: 2xsal, super eagle, ect.
Sorry, I only tried it with SNES game. I did not test it with a NES game with nestopia. I can test that in a bit. I am just putting up the mod right now. Once I put it up I will post and test out the shaders with a NES game. I will then take a look at the CRT-PI ones, to see if something is wrong with them.