iCloud is re-creating empty folders for old iOS Apps
It would help if you would explain why you would like to do this. For example, do you just want to clear up the clutter on your disk? Do you want to erase every trace of deleted apps?

If you just want to save space, the relevant command is brctl which is part of bird. (brctl for "bird control", as Apple uses the metaphor of the bird flying through the iCloud). At least according to the official documentation, the closest command to what you would be looking for would be brctl evict, but this doesn't remove the folder, but instead remove the local copy. In your example, you would type: 

cd ~/Library/Mobile\ Documents
brctl evict iCloud~com~FireproofStudios~TheRoom3


I would keep an eye on the brctl man page to see if they add that additional functionality for the future for getting rid of these folders entirely.