Baker's ammonia is an interesting ingredient. It's not so much that it's unwise to use it in recipes that don't call for it as to restrict its use to thin and dryer scenarios. A dry cookie, a cracker, etc. The reason for this is that ammonium carbonate (baking ammonia) will be converted to ammonia (a gas) in the heat of the oven. Ammonia is hydrophilic, and using it in a thick moist item like a cake can mean that traces of it are left behind. It won't poison you but it'll make your food taste bitter and gross. Thin, dry items can let the ammonia be baked off.
The worst thing that can happen is that you toss a few cookies away. I say you should try it and let us know how it goes and what you think. 
