Is there something special about the .Spotlight directories/data? I am nearly out of disk space and trying to remove old/unused files. I ran 
     du -k -d 2

in my home directory to attempt to identify candidates and found the following:

4   ./.Spotlight-V100/Store-V1
3297484 ./.Spotlight-V100/Store-V2
3297492 ./.Spotlight-V100


That's 6.6GB between them. I'd like to see if the V1 were still in use or just old.  But that directory is not viewable from iTerm ?

$ls -lrta $HOME/.Spot\*
ls: /Users/myuser/.Spot*: No such file or directory


That directory also does not show up in Finder even though I have enabled "Show hidden files".  

So what is going on with those directories - or are they truly inaccessible?
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.