Chocolate coating for truffles shrinks as it sets - What to do?
Maybe use slightly less filling?

You're forming the ganache balls freehand, you mentioned, so it might be possible to form a little pocket or gap somewhere in the filling as you roll it (maybe with a toothpick), so that when the chocolate shrinks there's space for the extra filling to go instead of bursting the shell.  I think it would work better if there was a way for the air to get out - a pinprick through the chocolate to the air pocket, which can be covered over after the fact by a dab of chocolate or decoration.  But if the difference in volume is small, it may work without that.

Alternately, you could control the effect by piercing the truffle through the chocolate coating, say, on what will be the bottom as it sits.  A little filling will probably leak out when it cools, but that can be scraped off, the hole will be small and controllable, and again - covered up with just a dab of melted chocolate or other decoration, if you want.  Much less chance of cracking or other visible damage.

Finally, you might try dipping in two layers.  If there's a gap, however small, for the filling to equalize out of your first shell won't crack or puncture - and a larger gap will have a smoother curve.  A second thin shell, overlapping and smoothing over the first gap, should render it nearly invisible.  You could dip about half at a time, or three quarters for a bit more overlap, or almost the whole truffle twice over for more chocolate per truffle, as you prefer.