How to Access
To enter secret shops, give one of your characters the Member card. To get the Member card make sure to recruit Rennac in chapter 14, as he is holding the member card.
Only characters holding the card can enter the shop.
In-Chapter Secret Shops
Note: Secret shops are found where the Erika sprite is
Chapter 14: Queen of White Sand (Erikias route)

Chapter 14: Father and Son (Ephraims route)

Chapter 19: Last Hope (Both routes)

Creature Campaign Secret Shops
After completing the game first time you will have access to creature campaign mode, from here you can access shops including secret shops that sell stat boosters and promotion items.
Choose the "Enter ????" option, then select the character holding the member card. Below is where you can find these secret shops:

Rausten Court:

Jehanna Hall:

Grado Keep: