DO NOT TRY TO DELETE THE CERTIFICATES!
You will cause more problems than you 'fix' if you succeed. HTTPS will break for one. I'd be surprised if RemoteApp worked at all. The problem isn't caused by certificates at all, it's squawking because you're using a self-signed certificate. Certificates are meant to essentially verify identity (among other things, but I'll be brief). Your system currently has no way to prove its identity via a reliable source, so it generates its own self-signed certificate.
What you can do is add the self-signed certificate to the machines you're working with. Take a look at this TechNet article. You can also do this via GPO.