It's safe to ignore that warning. Git is a little overzealous about when it gives out that warning.
We're currently working on making our automatic garbage collection smarter, so you shouldn't need to do this manually.
As for slow command line performance, try running git gc --aggressive and git prune locally. If that still doesn't speed things up, you might want to consider putting less data in your Git repo (Git isn't fast for every kind of repo).
If you're still running into issues, let me know. Thanks!