I cannot reproduce your problem. The passenger number is always asked if the estimate passenger option is Disabled.
However, if you make a flight and land on an airport, and choose Deboarding, if you already had the passenger number from the previous Boarding, it won't ask you again.
This is the only change from previous versions (in which it always asked), and of course it's an improvement, since it doesn't make much sense to ask if you still have the same number of passenger on landing, unless you would want to simulate something like a passenger who was thrown out/parachuted outside, which would result in a decrease of passengers, or a pregnant lady giving birth in flight, which would result in an increase of passengers...