I have never been on the dining plan, so I can't discuss use of snack credits. But I can tell you the quick service places where I have found cupcakes.
Epcot's Future World:
Starbucks (Fountain View)
Electric Umbrella
Sunshine Seasons Food Court downstairs in the Land, but it often has a surprisingly small selection
Epcot's World Showcase:
Karamell-Kuche in Germany
Kringla Bakeri in Norway but I think that might be closed
Animal Kingdom:
Starbucks (Creature Comforts)
Zuri's Sweet Shop
Hollywood Studios:
Starbucks (Trolley Car Cafe)
Backlot Express
Catalina Eddie's
ABC Commissary
Rosie's All American Cafe
Magic Kingdom:
I haven't been on a cupcake search in this park in a long time, so my list isn't great
Main Street Confectionery
I assume the Starbucks (Main Street Bakery) has them but I haven't checked
There's a gift shop in the new section of Fantasyland which has them
Boardwalk:
Boardwalk Bakery
Boardwalk gift shop
Hotels:
Yacht Club gift shop, refrigerator section
Beach Club gift shop, refrigerator section
The Mara quick service restaurant at Animal Kingdom Lodge's Jambo House
Those are the only hotels I have stayed at lately. I have heard that the Contemporary and Pop Century also have cupcakes.
This was the thread I used to enjoy but nobody has posted on it in a long time:
https://www.disboards.com/threads/show-me-the-cupcakes.2702083/page-57