As far as I remember, when Kaer remade Molten into Warmane, he admitted in Q&A that the old Molten did actually manipulate the server population, but he also did say that it will not be the case on Warmane, the new server. I hardly can believe the Warmane is manipulating the numbers now, because just by looking at Dalaran, it is pretty clear they are not. You literally find players everywhere.
It might not be EXACTLY 12,000 players online. Of course, there will be some miscalculations and delays in calculations as all machines/algorithms make mistakes with huge numbers. All we need to know is that we have nearly 12,000 players playing, which is astonishing.
But I do agree.. Limitation on /who and chat can be very frustrating sometimes. Especially if you are using addon called WIM (Wow Instant Messenger, it automatically does /who whenever you get a whisper from somebody), it is very frustrating to see sometimes the player information section on the messenger is completely empty and bugged out because of this limitation. If it is directly related to server stability, I won't complain. I rather play on stable MS than not being able to come online at all.
P.S. EVEN if they are manipulating the number, I am glad they actually are, because many players look at the number of players and come to our server! Might be frustrating if you are a non-donor account though :/