Nicholas,
The airline may use actual baggage weights or they may use figures that each bag weighs the allowable baggage limit, 10kg, 15kg, 20kg etc.
Check-in closes X amount of time before departure, that's when the payload is calculated and these figures passed to the crew, because Ops, at the flight planning stage, would have exaggerated figures, but not by too much, the aircraft should have been fuelled for a slightly heavier payload than the actual payload. In the event of no-showing passengers then the aircraft has more than enough fuel on, better to have too much than too little fuel!
I've never worked for a lo-co but I guess they use nominal figures whereas X% of passengers will check-in bags weighing Xkg each and these figures, at the flight planning stage, should be exaggerated also but on a 25 minute turnround, and check-in closing 15 minutes before the aircraft is actually on the ground, the crew can receive the actual payload figures before fuelling the aircraft.
Should a passenger, that has checked-in, not board the aircraft then there is a security risk if that passenger's bag is in the hold, then all hell breaks loose and they need to find the passenger or offload the bag. When the cabin crew do the head count is it to ensure that the actual figure matches the loadsheet figure to establish that no security risk exists and they can close the doors etc.