Yes, there is a difference. Hinges will try extremely hard to be in the correct position. If something gets in the way, they respond with unreasonable force. All the warnings about interpenetration and all that.
That's why things bug out in Lumber Tycoon 2. If you're in a trailer train going down the mountain with a large log load, and a log stays back for a split second, it forces the trailer wheel to interpenetrate throwing everything into disarray.
Joints/Constraints on the other hand:
They're pretty cool about not being in the right place, and will spring back. It creates a smoother experience and that's why I had so little trouble assembling the 70-strong trailer train. (In fact, the only issue I had with the trailer train was one of the wheels getting out of its wheel well. I managed to pop it back into place by dragging the trailer around).
EDIT: to further clarify, I did an experiment with the joints, and here's what I found: a little phantom energy is applied to the system upon overconstraint, compared to a lot of phantom energy when a hinge is overconstrained.