Most kinds of paint can be easily scratched from plastic, and marker style paints WILL scratch if not treated well. I would think that it would come off quickly on Legos all thrown in a bin together.
I had a little plastic Barbie television as a child that I pulled the "screen" sticker off of. My dad used a permanent paint marker to draw The Little Mermaid on it so it for me, and he had to touch it up soo many times because it scratched off.
I think a regular sharpie would work better.