I'm all for tunnelling, and I'll tell you why: When I first started playing DF, (before I knew better) I assumed it was already a part of the game, and I really got a chill when I started spotting several Antmen outside of my soil-based underground farm (the main source of food for my fortress, which had been difficult for me to set up).
I immediately posted several guards, and I really gave the possibility that they might break in to my main food source, a lot of thought. It was exciting! It added to my game experience, especially considering that I thought it might be possible that once 1-2 antmen showed up, that they'd (like ants do in real life) lead the rest of the antmen back to my farm and attack it, en-masse.
It's therefore been my personal experience that this is likely to lead to a better, more immersive, gaming experience.
I *will* strongly qualify it with the statement that I absolutely think you should get a message about enemy miners/sappers in your area, WELL before they come anywhere near your Fortress. Like anytime anyone other than a friendly dwarf starts digging into the solid structure of the stone surrounding your Fortress, to a depth of say 12 squares in any direction. That should be a racial dwarf ability.
I also think that the vast majority of animals and primitive humanoids shouldn't be able to dig into anything but soil, and that all of them-except for a few special exceptions, specifically antmen-should dig considerably more slowly than dwarfs, with a greater chance of cave-in.
Humans and goblins (goblins with the help of trolls, anyway) might be able to tunnel into stone, but again, it should be a *lot* slower than dwarfs, and they shouldn't get a warning about counter-sapping or enemy tunnellers.
Cave-ins and other disasters should, again, be a lot more frequent, and a lot more dangerous for them.
Also, as briefly mentioned, there should be counter-sapping options.
Things that come immediately to mind include:
salt-acid traps (melt your enemies, for fun and profit!),
rigged boulder traps that don't even require mechanisms, and are just waiting for someone to mine under them (easy squish),
"stone" that is, in reality, a horrible grey ooze creature, or a living, impaling, stalactite creature, or an earth elemental with a hangover, or the fossilized shell of a giant undead anemone, or...well, you get the point (and the goblins will, too)
Swarms of snakes, scorpions, fire ants, 'The Mummy' style scarab-beetles, undead carp, horribly deadly black mold, and anything else that lies dormant-but ravenously hungry-that your dwarfs can "seed" into a tiny hidden pocket of soil, until some idiot pokes it with a sapper's pick (don't let that idiot be you!)
Traps that only go off if a wall is breached, perhaps dropping a sarcophagus that is solid on every side *except* for the open one facing the breech, and that contains your choice of: zombie minotaur, tentacle demon, lavaman.
The same trap, only with a funnel at the top, from which flows an unending stream of: coal smoke, extremely fine sand, bees.