check how many certificates you have in Machine's personal store.
Start > Run > MMC.exe > file menu > Add/remove snap-in > add > select certificates > Select "Computer Account" > Finish
From Left Pane > Personal > Certificates
see if you can remove certs from there.
Just take a backup and delete what you think is old enough to discard. Restart the server. and keep watch for anything breaks.
If you want to be very much sure of it that you delete correct files.
Monitor if any process/service is using any of those files.
I would just start the process monitor or file monitor from sysinternals and then configure it to filter access to that folder and keep it running for few days. This should give very good idea of which files among those thousands are being used.