I don't think your airbrush is in Windex long enough to do any damage to the seals. Most of the time mine go through 2, 8 min cycles, and that is it. I don't let them soak in the Windex any more than that.
Been using mine for a few years, and hasn't harmed the seals. There is so little ammonia in Windex that I don't think there would be any harm.
Now if you were using straight ammonia, might be another thing. Then again, buy a bottle of Acrylic cleaner, like Vallejo's AB cleaner, and just use that bottle for your sonic cleaner. When done, pour it back in the bottle, and use it again next time. If you are worried about sediment in it, run it through a coffee filter first.