I've been dealing with the same issue for the last week or so, but just found a solution!

Install the GitHub CLI ("brew install gh" or similar), authenticate with your GitHub credentials ("gh auth login"), then run the following:

gh api --method PUT -H "Accept: application/vnd.github+json" /notifications -F read=true

Blue dot gone! :-) This marks all notifications as read, which clears the phantom notification from the deleted account.