There has been reported issues with annotated PDF files remaining ... not removed ... and space usage. From what I can tell, no resolution to that issue.
Deletion of anything in moodle is of concern ... deletion of users from backend does create issues in other areas ... like files that belonged to the users deleted. Always best to find a way to get moodle code/cron/adhoc task jobs to do it.
As far as space usage ... yep, if moodle is used, it only grows in the needs for more space/processing power etc. moodledata doesn't need to be on same server (am sure you are aware)... so if the web service isn't really stuggling to keep up and it's a space issue, moodledata could be on a server dedicated for storage of filedir - just a mount point for moodledata/filedir/ where the other directories in moodledata that require speed remain on same box as web service.
Have found that using git for installation/updates/upgrades by far is less stressful for those who wear that hat - and does make it less stressful for those involved in other areas of moodle server support as well.
Much also depends upon plugins ... and themes are plugins.
Any entity today certainly has options for their online learning options and the two you mentioned have made inroads in the K12 world (at least where I live). But, like anything, there is + and - to any choice.
Did you get moosh to work on your server?
'SoS', Ken