Dust vs. Undust?

Undust is used so little that you should indeed see it as obsolete. That ngram shows some results is not really relevant if you compare it with the occurences of dust.

Your paranoia is uncalled for, there is really no proficient, let alone native, speaker of English that will think that dusting your keyboard is similar to watering your plants.

I can understand where your hesitation to use it comes from, as you seem to be saying to opposite of what you are doing. Actually, to complicate matters, dust is used in the sense of adding dust as well: lightly dust the cake form with flour.

In context, however, there will usually be absolutely no confusion. When you dust your keyboard, everyone will understand that you are cleaning it.

As to the logic behind one word meaning two different (opposite) things, we are talking about English, the language that uses words like inflammable, and in which people say I could care less when they mean the opposite. Don't get stuck too much on logic when it comes to natural language!