I use windex on the outside glass as well, but I observed a funny thing. When I actually sprayed the Windex on the cloth in the same room, my fish briefly freak out a few minutes after I do it (with no lasting apparent harm). I started doing the spraying of the Windex on the cloth in another room, and noticed much less distress on the part of the fish.
I am guessing, but maybe it's possible that enough ammonia gas gets into the air, and then dissolves in the water, that the fish notice it? Or maybe it's the fine drops from the spray that float around and actually land in the water somehow. Either way, I don't spray from the bottle in the room with my fish any more. I just bring the Windex dampened cloth in to wipe the glass.