Anywhere except Malcolm's house and the room in the Ducal inn in Verdists are fine for storing items; some people have had problems with these locations, though buying/re-renting often fixes that.
Somewhere close to a teleporter pad and/or your favourite merchants would be a convenient place to store your stuff. You can lock a chest by using Lockpick on an unlocked chest, but there is no need to; you can leave stuff in containers or on the ground without fear of anything being stolen or disappearing over time.
