So from what I understand GA members get 6 and non-GA get 3 shops/galleries. What happens when a user's GA expires and they have more than 3 shops/galleries?

I think your extra shops are still there, you just can't add to them until you get a GA again. But you should be able to remove things from them without a GA.

Oh that makes sense c: Do you perchance know how is it determined which shops can have items added to it or not?

Hmm, I actually don't. But I would assume that it would maybe count the shops that you created most recently to be the excess ones. So probably the ones with the higher ID numbers.