Yes and no here is a breakdown:
MK1 -3 wagons are heavier since they need to e a bit balanced in order to compensate the larger amount they can carry , it is a linear scale if i remember well
So yea with a larger load you are slower and it all makes sense.
o another side normal ones have a lower max speed cap then MK ones so with certain combinations of fuel and or MK locomotive the normal wagons WILL hard cap your speed.
Any other questions?