There is luckily enough a Pokestop close enough to my workplace to check-in every few minutes. This yields me the necessary Pokeballs and experience, but my bag is getting full. I am only allowed to have 350 items. Are there rare items (so no Pokeballs) that I would miss out on with a full bag? Is it a good habit to not check-in very often to keep an empty bag?
Just keep using the Pokestop. If your bag is getting full you can bin a few pokeballs, don’t worry about binning them all since it asks you which amount you want to throw away.
This way, you can keep getting exp and chances for the rarer items which you do want to keep. Good luck!