Yes. Hydrometers take readings from the air inside the humidor, so it is very likely that different sections will have varying Rh. It will probably only vary sightly, so it shouldn't be a problem. You're reading a higher Rh on the top level of your humidor probably because there is actually more air circulation there.
In my experience over stuffing your humidor can make your Rh seem low, but my cigars are fine. If your sticks are smoking fine don't worry so much about numbers.
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