Hmmmm...
Well, Google says it's also associated with childhood and simple pleasures. It is also an easy and affordable meal in times of economic hardship. While none of these concepts are particularly related to humor, they do have the potential to bring smiles. It's also possible that the nostalgia aspect could remind ponies of the childlike wonder that they once had, which includes their hyperactive sillyness. On another, less deep, note, grilled cheese is a random object, and random objects are often affiliated with whimsy.