I think the logic would be that if the USB connection gets pulled by a reasonably large force, it's safer for the device to unplug rather than being really solidly connected.
Have you used USB C yet? It's a much improved connector.
Indeed. USB is designed so the "spring" is on the plug which makes the sockets last longer (a very good design decision as cables are cheaper than replacing sockets which may be soldered to the board), so poor cables often give the impression that the socket is bad when it isn't.
USB has been very successful and cheap. So much better than the RS232 it replaced. A 25 pin connector for just serial data. Mostly a pain, it did have one advantage. The connections were effectively outside the box. This is better for stopping water and mechanical damage. So no I don't think connectors should be deeper. In fact they would be better not intruding into the equipment.