Once you beat the game, you can enter the shops easily. First, get a membership card, then go to Grado Keep and enter the shop.

I know there are at least two on Eirika's path. One of them is on Chapter 14 in Jehenna.
To the left of the throne is a green upside-down "L". Go all the way to the top, and go
as far as you can to the right. Then there should be an option that says "Secret" or
something.

There is also one on Chapter 19, I think, but I'm not sure where it is.

I've only completed Eirika's path, so I only know where her Secret Shops are. Good Luck!