Maybe in DF the trees have to be cut in a certain way that only the Elves know to be okay in their moral code?
If you ever traded with the elves instead of magmaing them on sight, you would have noticed that they bring "grown xxx-wood" stuff now
... dwarves' biggest threat would be other dwarves, and once intra-race wars are implemented, we'll be seeing them a lot more I'm sure, due to dwarves all wanting the mountains.
A possible defense would be a "sheath" of empty space around a fortress, filled with magma or even water, and with sealable marksdwarf positions carved into the fortress-side part of the sheath.
While this makes for a nice and hard-to-pierce extra layer of defence, it can still be defeated by a clever attacker. You'll have to be prepared for it by offering a drainage tunnel of your own when breaching the shell, but if you do, an entire wall of water can disappear in a matter of seconds. (Magma will take significantly longer.)
In addition, for dwarfs directed by a human player, the threat can be minimised: you'll get the damp/warm wall warnings when getting close, and you can reduce the damage of a breach by putting doors and/or depressuring blocks into your mines.
I once easily disarmed a doomsday clock surrounded by such a water sheath simply by punching a drain to the caverns. And the work invested in such a water sheath is enormous, while it can be taken out in probably a few weeks of mining if you have an idea of what you're facing.
Another mode of attack would be cave-ins. Not by undermining an enemy fort, simply by building supports with floor tiles on top and pulling them away. Cave-ins crash through floors until they hit a natural wall or mined-out staircase. Once you're on top of the fort proper, you can simply install a bunch of supports and smack them into the construction, as sort of shaped charges. Obviously, there are defences against this - starting the actual fort a good way underground, making checkerboard patterns of mined-out and untouched rock on each level. Still, patient siegers could get you eventually if you just try to sit them out.
Thinking three-dimensionally definitely gives some neat options in DF. One of my fondest military memories was when my dwarfs defeated a human force that had set up camp by digging out the floor under them and caving in the camp-site. Much easier to trap them underground, where you've set up everything to welcome them.