You can, and should, remove the downloaded binary files associated with legacy updates.
You can step through each vendor node and group by the file download status icon and then sort by Creation Date to identify older updates or you can do that in one pass from the All Packages node.
Use the "Delete Content" action to remove the downloaded binaries associated with those updates.
The other thing you can do, but will have much less of an impact, is to deselect vendors/product you do not need from the synchronization settings, and then delete those packages from the console.
For the unneeded packages that use PackageBoot, you can recover about 1MB per package.
Use the "Delete" action to remove the downloaded packages.
NOTE: If you delete a package that is in a catalog/vendor/product still configured for synchronization it WILL be re-synchronized at the next Patch Manager synchronization event.
This behavior is different from the WSUS server, which will never re-sync a deleted package.