No, Israel is having no such strategic problems. Israel is systematically destroying the tunnels starting with the access shafts.
I can’t cite the numbers with precision but recall that so far on the order of 500 of 800 known access shafts have been closed/destroyed.
The access shafts are located within the lower story of existing buildings. ( including the homes of Hamas leadership) The building is declared Hamas and then bombed. A bull dozer then clears the dust and chunks and rebar tangle to expose the shaft. A decision is made to leave, plug with a “sponge bomb” or destroy.
There is video of “micro kamakazi drones” that make their way through the tunnel until a spot for destruction is reached. The drone then explodes the charge it is carrying and destroys the precise tunnel location selected.
Since The IDF is going to occupy Gaza for the foreseeable future, it is not necessary to spend time and resources to destroy al tunnels at present. The destruction can be undertaken in a controlled manner for years to come.
Maybe even in the lower levels of “innocent civilians” abodes have access to tunnels.