Is there something special about the .Spotlight directories/data?
Yes you may delete those directories.

These directories house files that are indexes to allow searching your drive with Spotlight. (see the magnifying glass on the menubar of your Mac.)  Deleting those indexes will force spotlight to re-index your drive (which is perfectly natural) and it will make a new index, hopefully something small and tidy.  I've no idea why your index is so large and would hope that the new index will take up MBs rather than GBs.