How to anonymize self-citation of source code repository in IEEE double blind peer review?
I think most reviewers for IEEE Communications Letters are unlikely to visit your source code link and try and validate your code. It's fairly unusual in this field (I say this as someone in the same field.) Certainly the reviewers will not expect access to your code. So if you want to anonymize everything, that would be fine.

If you want to preserve the ability of reviewers to access your code (which is a very good thing!) and don't mind going to a little bit of extra trouble, you could always just upload an anonymized tar.gz archive containing the source code (without the version control metadata) to any file sharing site. Then use that URL in the version you submit for review. (When the paper is accepted, you can update the reference to point to your non-anonymous repository.)