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?
As you get higher level you get more different items(at level 5 you start getting potions and revives, I don't know if you get more different things at higher levels). But if you keep catching Pokemon you will use your pokeballs, so you can also use an incense to get more Pokemon in the area. You can also place a lure module which attracts Pokemon to the PokéStop.
So no, keep using the Pokestop, you'll get free xp as well