I have not heard of a shortage of prevention, but there is a shortage of treatment.
Immiticide is on indefinite backorder because Merial screwed up. Merial is rationing the remaining Immiticide to clinics that are actively treating a heartworm-positive dog. We used to keep a couple boxes on stock a heartworm is pretty common around here, but we are no longer allowed to order "just in case" stock. Even then, there's no guarantee we can get immiticide if we need it.
But, as for prevention, I have not heard of any shortage. With all the different types and brands, I highly doubt there will ever be a shortage of prevention. If all else fails there's always straight Ivermectin to use (for most dogs, anyway).