I've heard the assertion that waterbornes are damaged by Windex, so I did some experimenting. I coated maple plywood with four coats of Target's EM8000. I chose maple because I thought it would show damage most easily. I let the EM8000 cure for a week. Then I did the following tests.
1) Spray Windex on, and rub it around like I was cleaning the surface. Result: no observable effect.
2) Make three quarter-sized puddles with water, oil, and Windex. Wait two minutes. Wipe off. No observable effect.
3) Repeat the puddle test, but wait ten minutes. With this one, I could see some color where the Windex had been. The color looked like the maple had gotten wet.
4) Repeat the puddle test, but wait two hours. At the end of two hours, there was no observable effect at the water and the oil puddles, but the Windex puddle was nearly gone. There was a distinct "wet spot" appearance where the Windex had been, and the surface of the finish there was bulging out of the plane of the rest of the wood. It looked like the ammonia in the Windex was somehow helping the water to penetrate through the finish. Five days later, the discoloration had disappeared. Presumably, the water had migrated further into the wood, or come back out through the finish.
My conclusion is that Windex does indeed have an effect on the EM8000. However, if it is used the way it is likely to be used, the effect is not significant. That is, I won't let fear of Windex chase me away from this waterborne.