There isn’t any easy way to auto-remove everything below a certain length. But if you have a list of existing tags you can use the tagging tools plugin - https://github.com/svivian/q2a-tagging-tools
First you can set the minimum tag length to 3 to prevent short tags being added in the future.
Then in the textarea add the short tags you want to remove, one per line, tick the conversion box and save. It will remove those tags from all questions.