Hi Slicepong,
Yes it can be tricky to judge depth in shots and this can cause mistakes in your returns. The best way is to always expect the ball to be longer and look to topsin as your first choice. This way if the ball does go unexpectedly short you can still step in and reach it with a push or flick. If you expect it short and then it comes long its very difficult to step back out and react to play a topspin.
Another key is watching the contact and the flight of the ball closely to allow you a better idea of where it will land. But the main area to focus on is my first point about expecting the ball long and stepping in if not.
Give that a try and let us know if you find any difference and stops the hesitation for you!