I can only partially answer to this one.
How the passengers appear on some airports wishing to fly here and there... only they know

!
On the other side, whenever a pilot performs a PP flight, it is assummed he flies the aircraft with as many passengers as possible, and this number is deduced from the "waiting passengers".
This explains why on certain routes, very popular among pilots, there are no waiting passengers: all have been already served.
Now, doing a flight with a full plane has indeed a small incentive (passengers sum up in a "whole carieer" counter in the pilot stats). However, it is not the intention at EHM to discourage flights performed with a low load.
This would lead to connections like "I cannot do this flight because someone else did it before me, grabbing most waiting passengers" - which is not how the PP system is supposed to work now.
Personally I am looking at the waiting passenger numbers when I decide where to fly to but always use this as a low priority criterium.
One last comment, currently there is no connection in PP between flights and their return counterparts. A pilot doing a flight has no obligation to do the return flight as well. As a consequence, you can find a lot of passengers at airport A willing to go to B and none on airport B willing to go to A.
In this situation, I think we should not ignore the unfortunate virtual people on A and ruin their virtual businesses, holidays etc. only because there is no virtual money to make on the virtual return flight

Andrei