Will ammonia based window cleaners damage your vehicle. The quick answer is no. They will however do some damage to old rubber parts and paint that has seen its better days. Rubber that is hard and or cracking will be damaged, treating the item first may lessen the damage. Old paint well not a lot for this.
Also if you leave the cleaner sit on any item or paint it may do some damage which can generally be removed with several methods. There are several cleaners on the market without ammonia but they will not clean as well. There are several home made recipes on the net, but I have not tried them so I wont recommend any.