I bet it is because it goes under peoples homes and businesses on the way to mexico. People who are not involved would be pretty peeved if the government blasted the dirt out from under their buildings.
This may not be the situation but I have no other reason to offer why they dont just blast em shut.
The tunnel is only 100 yards. Look out your backyard and estimate that's only the length between your house and both next door neighbors. Add a river down the middle and the only thing that would be damaged in collapsing the tunnel would be a few spiders and scorpions.