Patches are only download during the deployment phase, so these patches were either deployed to machine that required them or someone manually download the patches through the UI. Feel free to delete everything from the patch repository, patches that are required for deployment will be downloaded again when needed. The default location would be C:\ProgramData\LANDESK\Shavlik Protect\Console\Patches.
You can filter out product from your scans which would in essence limit what is downloaded, but you would be ignoring patches that may be needed. Keep in mind Protect only downloads patches that were detected missing and only during the deployment processes.