Israel probably has 200 fission nuclear weapons. No fusion (thermonuclear) weapons, as they are much more expensive and difficult, and they have no enemies big enough to need one.
This being said, what they need in this case are thermobaric or fuel air explosives. Much like killing gophers in a hole, you spray a lot of propane gas into a tunnel, then toss in a hand grenade. First, there is a massive overpressure, as all the air inside the tunnel is combusted, then the ceiling and walls collapse.
In their place, I would get a heavy vehicle with a large propane tank strongly secured horizontally in the back, with a quick release pressure valve. Spray it down the hole (propane is heavier than air), until about 10 pounds of gas are down there. Then move away from the tunnel entrance and pitch in the grenade. Pop.
If there is equipment or weapons down there that have to be destroyed, you use a thermobaric weapon to raise the tunnel temperature to perhaps 800-1000F for some seconds.
I know for a fact that they have both and in the numbers I stated earlier. Their SLBMs are nuclear but they have the big boys, joining the elite club of only about half a dozen nations.