I don't use the device itself to buy books. For the most part, I don't mind the store stuff being on the device. I prefer it to be kind of hidden away though. For example, I don't mind there being a "Discover" tab on the homescreen because I don't have to click it. I don't like store book covers taking up space on my homescreen. That's annoying but not a deal breaker.
I do buy books from the Kobo website because I can never pass up a good coupon. I wish the search functions were better though.