I'm now happily employed and wondering if I should clean these out, or leave them so my 'contribution history' shows the time I've spent learning?
I don't see any reason why you should delete them. They contain code and code snippets that you've made and that someday may prove useful to reference or reuse.
Also, given you are already hired, I don't see how this could end you fired, or reflect badly on you. In fact, this would tell me "wow, this guy really likes to code, try new things, and learn on their own".
FYI, and without intending to promote any product, Atlassian Bitbucket offers unlimited private repositories. Surely alternatives exist if this one is not of your liking. You could consider moving or copying your Github repositories there, so they are private and there is no chance of anyone randomly stumbling upon them.
That way, you can leave on Github the ones that are completed or you feel comfortable showing to the world.