Just did my first B&E into a shop. I remember in previous versions that weapons and merchandise were all over the shops to steal. However, I don't see anything in this shop worth hitting. I did hit his cash box for some gold but no weapons, armor, magic items, spell books...nothing.

Where are they?

Modders will sort this out.

Different shops have different merchandise.

Simple as that.

Clear everything off the shop shelves - either it's reasonably valuable (Radiant Remnant), or you can use it to increase skills (Blacksmith in Riften).

Storekeepers keep all their money and inventory in a hidden portal only they can access. No morrowind store inventory chest.

steal everything. dishes food clothes, its all worth something,
and dishes and food are usually pretty valuable when
compared to how much weight they takeup and there is usually a lot of it

Yeah it's sad you can go into a shop and not be able to steal the prize possessions....