There is definitely no fuel saving if you have a non-stop as all the fuel needed for the flight from SIN to DPS would have to be carried all the way from AMS, which would need loads of extra fuel just for the transport of the fuel. (And that extra fuel would have to be carried all the way from AMS too, which would lead to even more extra fuel, and so on.)
This is why there exist no non-stops between Europe and Australia, for example.

In our case I reckon the stops are mainly a question of demand. Once GA has become part of ST and CGK has gown as a hub, KL will certainly offer AMS-CGK non-stops.