These are unlockable shops:
"Atelier Saibara": ship a load of clay
Hearty Lyla: ship gift items
Blacksmith: ship ores
Flower Bud Library: opens during spring of year one
Moonlight Café: opens during the summer after meeting Duke
Perch Inn: opens during the summer after meeting Doug
Café Callaway: opens up one month after meeting Carl and Eve
Sanatorium: ship 30 herbs and have Alex with at least 1 heart