this is probably not a good program to start with because they more technical, but i feel like i should mention that vector programs like inkscape have built in bitmap tracing i believe its called, that you can have it automatically detect linework from a scanned image, so you dont actually have to redo your lineart. but the lineart has to have a lot of contrast between the page for it to work well.
but you basically can cleanly bucket fill the cells where it traced afterward. vector programs dont use pixels, rather curves, so the coordinates for each point in a line is what it renders an image with, so coloring is a lot more crisp looking. i'd have to see how different inkscape is since the last time i used it in 2014, cuz its possible it's more user friendly now. but yeah i would recommend learning a raster program (programs that use pixels, not curves) like gimp or krita first but your mention of linework made me think of it