The .rar files are the files containing sample sets and other files used to install the virtual organs: HW's installer uses these to set up the instrument within your HW system. Once the virtual organ is installed these .rar files are not actively used by HW but should be stored safely so that you can use them again to install the virtual organ. I keep all of my .rar files on a separate disk (and back this up too) to save space on the disk containing my HW system.
The HW uninstall function removes the components which have been installed from the HW system, this can include sample data, organ definitions and so. It does not touch the .rar files. (I assume it also removes the cache for the instrument being uninstalled, but I've never checked this.)
If you have several drives on your computer you can (re-)configure HW to put some of its files on the other drives (see pg 19 of the HW user Guide) and this can save space on your "system" disk.
I hope this helps.
Iain