can you even destroy tunnels?
Theoretically yes. I could scan for the health of a tunnel door. If it's 0, tunnel will be out of order.
Will this remove the stats of the units like kill count?
No, it will not remove any stats. This system only sets the squad invisible during the transport, to simulate the tunnel. The squad coming out of the end of the tunnel is exactly the same as the one going in. NOTHING has changed.