My thinking on a per-device basis was that themes might work better/worse in a mobile vs. desktop browser, so people might prefer different experiences, but I could see the other side of things as well. That was also the rationale for making compact mode be in the cookie rather than saved in the db.
I honestly don't know what the expiration of the session cookie is. It might depend on the browser. I think it is pretty long-lasting unless people clear their cache because I have definitely loaded up piefed instances after a long time and have still been logged in.
As for technical details, to save space, it might make sense to make a key (maybe like ignore_comm_theme) be a comma-separated list of community id's that people have unchecked the box. That means you can easily convert this to a list with split and then see if the currently requested community id is in that list. Being the id means that it is unique for the instance and avoids name collisions like the actual community name might have (how many linux communities do we have now). It also keeps things relatively small since the cookie has a pretty small size limit iirc.