It'd be an interesting challenge, and fun to defend against.
Really, boiled down, this is the essence of the argument, it seems to me. Whether or not we ever get Tunneling, in whatever form, we've still got people/creatures/monsters/what have you, attacking our fortress. Sure, they do it by going through the air, or in some cases the water, but all Tunneling is is adding another medium through which they can attack you.
Noone's arguing against goblin seiges or random monster attacks, but Tunneling is really just more of the same. That means it's something we will be able to defend against.
I suspect that, when Tunneling gets put in, we'll see good defenses
against Tunneling put in, also. We won't suddenly find ourselves naked and without recourse. There might be new traps, better squad control, all sorts of cool tools to play with, that come in with Tunneling, and that make the game (and our fortresses, themselves) more interesting.
And in the words of Urist McBadass: "Our homes are not defended by these stone walls alone, nor do we hide behind them. Our homes we protect by the weapons we wield with the strength in our arms, the will of our minds, and the power of our unmovable conviction. Our homes are defended not with cold stone, but with the hot life's-blood that pumps in the veins of every dwarf who lives here, from the first to the very last."