I dont think the age of the aircraft has anything to do with weight restrictions. I know CAL has to weight restrict on flights from EWR to DEL, HKG, etc and thats on brand new 777s!
There may have been a number of reasons why there were empty seats:
-the flight checked in full but people missed their connections at SFO. When you check in for your flight PodunkA-Hub-PodunkB you get checked in on both flights. Now if your flight from PodunkA gets delayed and you misconnect at the hub the computer still has you checked in Hub-PodunkB. This happens a lot at hubs (such as SFO) and gives the gate agents the impression a flight is full. I usually don't put much faith in that estimate because there have been more times than I can count where either I was jumpseating or had a jumpseater who was told "the flight checked in full, you'll probably have to ride in the cockpit" and then when its time to close the door "oh hey guys, looks like I've got a seat in back".
-there may have been some "must-ride" bags or freight that the company deemed it more valuable to move that then passengers who could take a later flight.
-passengers may have been traded for fuel on a flight where delays/weather were an issue. Easier to inconvenience 3 people than 50, right? If the fog was widespread (as it tends to be on the pacific coast) it may have been a long way to an alternate airport with suitable weather which requires extra fuel to keep things legal (and safe).

So on and so forth. Just remember, with the airlines things are not always as they seem