I have connected through from North to South to get on Air Malta and have found the area mostly empty. Once the bus gets you to the South terminal, you go upstairs through security where they check to see if you have a printed flight confirmation of an e-ticket or a paper ticket. Once through security, there is a counter where the various airlines have desks. The only significant line (maybe 20 people) that I have ever seen there is for Continental flights.

My only experience in this area is around 8am after arriving at the North terminal on the overnight flight from ATL. The Air Malta person usually does not show up until around 8:45am so I always have to wait for a little while.