No downside that I can think of, especially if you have changed all the meta data in the template code. Adding an original header and footer would benefit you also.
If your sites are getting traffic, why don't you place a short poll on them to ask your visitors about their experience on your site so you can make improvements. It's a good way to interact and keep them on page longer.
Go for the colors you like best. After all, you paid for the theme and they are your own sites. As long as you mix up the headers a little and like you said, make each a little different, it's absolutely fine.