You can't possibly make matters worse, and probably can't overkill it either.
I've tried to find some recommendations and the only thing I found was a recommendation of 1 sq in per 1K BTU burner. This is for naturally aspirated burners which yours is mechanically aspirated. For a naturally aspirated burner, 2 each 6" diameter openings would be very close. The draft induction blower has to pull in the same amount of air it exhausts and I believe your original idea of a 3 or maybe 4 inch would be quite adequate assuming the internal construction of the water heater will allow free flow to the blower intake.
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