Scooter lead acid battery
All sounds normal, presuming the charger is poorly regulated and you measured it without a load. 

1) See the voltages on the battery label! 40V/3 is within that range.
2) The charger can provide up to 45V (15V x3 - see that label again) under load. It may well be 48V when unloaded, check it again while charging.
3) Only 2 pins needed, so sounds normal.

So, test the batteries.

Take a lab power supply, set it to 14.4V and current limit to 3.6A (or less) according to the battery label. (Or use a 12V battery charger if you have one). Charge each battery individually from that until the current falls to 0.5 or 0.25A or some such figure.

Then connect a 12V lamp (or some other load) across each battery and see how long it lasts : if the load takes 2A, double the time to get the capacity in amp hours. Replace any battery which died much below 12Ah.
If they are all a bit low, replace the lot - anything else is false economy.