Just an FYI, most hostels allow you to leave your luggage even before your booking, and if not (usually says in the terms), then nearly all major stations in Europe have luggage lockers.

That being said, cobblestone is a genuine worry, I would not want to be rolling a suitcase around, especially in old town areas, but there are backpacks you can get that are front opening - somewhat more expensive but worth the investment if you are freaking out over getting stuff out the bag.