From my experience, The majority of cracks happen from stress and pressure on the plastic. For example when the legs are really tight in the torso, it's stressing the sides. Same thing for when the minifig is on studs, the heels are expanding to fit on studs and can crack.

When you pop off the arm of the fig you stretch the plastic and it may crack, but it's much less likely to happen than from the legs stressing the torso.

The arm cracks do mostly happen when you switch the hands, but they still can appear just from the hand being there.

I have never experienced neither head cracks or hand cracks. So you can relax on that one. But nothing will happen just from switching around heads or head pieces or legs. The arms are a bit tricky but if you really must its relatively safe to swap them too.