You might use an analogy with a real warship. The CIC of a modern warship might have 30 or more stations, and at action stations, every seat would be filled with likely a few more hanging around, depending on the ship and the navy. During a normal cruising watch, there might only be a handful manning the essential systems for being underway; radar, comms, sonar, and so on.
When you see the interior of Normandy (SR-1SR1 or SR-2SR2) and have the ability walk around, it typically isn't in a red alert/action stations situation. It's cruising or conducting routine flight operations or quietly docked somewhere. So it makes sense that most of the stations are unoccupied. The times you do see the interior of the ship when it's in combat, (the Battle of the Citadel in ME1, the attack on the Collector Base in ME2, and in ME3 the assault on Earth), you don't get a full view of the interior, so you could be safe to assume those empty positions were filled.
As for why SR2 seemed to have more stations than crew, Cerberus might have intended more crew but were limited because they specifically chose Cerberus personnel that Shepard could get along with or sympathize with (which was explicitly stated in one of the games), which may have limited the available pool of personnel.