Hi Angela,
My family have never encountered any problems at all in exchanging counter-service meal credits for snacks during previous visits.
If you have counter-service meal credits left at the end of your stay, I would highly recommend a trip to Goofy's Candy Company at Downtown Disney. Although items are always subject to change, I can tell you that we have been able to exchange our credits for rice krispie treats, animal crackers, pretzels, candy bars, lollipops, gingerbread, cotton candy, several kinds of nuts, cupcakes and various pastries at this location during previous trips.
While eligible snack items are generally marked, my best advice would be to ask a Cast Member to point out to you all of the items that are eligible to be purchased with your remaining credits.
It is also worth noting that during my last visit to Walt Disney World in October 2011, we were able to exchange 1 Quick-Service meal credit for 3 snacks at the food court in Disney's Port Orleans Resort - Riverside. This however could only be done in the food courts and It was not possible to do this in the gift shop at the Resort.
I hope that this information has been of use and assists with the planning of your next trip.