You should be able to use as many colors as you want, since computers aren't as limited as cartridges. If a computer can handle it, the sky's the limit. You probably won't need much more than 16 colors on a sprite though (unless it's really exotic or something).
Hey, sorry for bothering you but I have one more question. I'm making custom sprites and I was wondering if there is a palette limit of 16 like in rom hacking, or can I add more to the palette?