As far as I noticed, it does not help you to spend your time in the game by doing whatever. Means: items in shops do not refresh if you lets say "just stand around" or doing missions and spend 24 hours ingame-time. The item-refresh only works if you use the ingame-option to skip time in the menue. Skip at least 24 hours by using this option and then shops will refresh their items.
Watch out: some shops and Ripperdocs have special offers like blueprints or weapons and clothes etc. when you enter the shop for the first time. So you should have enough money before entering the shop or you need one of the many possibilities to make "quick money" while your first visit (I'm playing on PC by the way).
Hope that's understandable and helps you.
Greetz!
CW