This is fantastic, thanks for investigating. Not a critical issue, but a useful one, in my opinion. I'm going to report it to the RICOH THETA product manager this week. BTW, I followed mostly the same steps, but I skipped using Mac Pilot and just used Mac OS X itself to show hidden files. All you have to do is run these two commands in a terminal window:
defaults write com.apple.finder AppleShowAllFiles YES
You'll get a quick BLINK of all your icons, don't worry. That's just the Finder refreshing.
If/when you get tired of seeing the hidden files everywhere, run the same command with "NO":
defaults write com.apple.finder AppleShowAllFiles NO
Looking at files on my RICOH THETA S it looked like this:
Interesting thing is - you mention this but I'm just re-emphasizing it - just Empty Trash on your Mac and all the files will be thrown out from your RICOH THETA S. This is what it looked like after I did that:
Saved me a TON of space on my camera. Very cool.