I've definitely used more than one color thread in my hand quilting. I try to make the quilting stand out - isn't that why we're doing this - at least partially? I'm very happy with the results. I try to use a contrasting but coordinating thread color.
If I have say red and blue blocks in the quilt, I'll use the opposite colors in the respective blocks. Or a white; yellow; whatever. I try to keep my quilting thread colors within the same color families within the quilt but use them on opposite blocks to make them stand out. Or, by contrast, use same color on color if I don't want those particular blocks/quilting to make a statement....if any of that makes any sense.