Does it hurt a large desktop Mac to be transported repeatedly?
Apart from the obvious risk of significant damage from drops and what not (which you seem to have taken precaution against), the only real vibration prone component of computers is generally the hard drive.

When a hard drive is shaken to violently, there is a risk that the read/write head will touch, scratch, and damage the spinning platter. However, in their off state, hard drives park the heads either in a "parking zone" in the very middle of the platter (where no data is stored) or on the outside, away from the platter. In this state, vibration isn't a threat, since the heads aren't able to reach any sections of the platters with data.

TL;DR: It's fine so long as it's off during transport