Ways to Make Surviving Sieges Harder -
Refined Fungiculture -
Current underground farming methods for producing crops that dwarfs favor do not require a substrate other than muddy earth. Fertilization is unnecessary; the mushrooms spring from the muck and in overgenerous quantities year after year. Aside from the obvious and well known issue of farming requiring far too few people and far too little space for what it yields, dwarfish fungiculture requires no raw materials to be successful in spite of actual fungiculture typically requiring a nutritive substrate (natural or otherwise) and lots of care. This means that it's completely possible and extremely preferable to make vaulted fortress farms immune to outside attack, because you don't actually have to go outside for anything, least of all food.
A solution to this could be to make fertilizer a necessary component of fungiculture. (Personally, I think this should be done for reasons besides making sieges harder, especially if dwarfs had distinct methods of growing things that set them apart.) Potash, compost, slabs of wood, flour, offal and carcasses, whole unprocessed plants; all of that could and should have to be used to make those plants grow underground. While green plants may grow in passable quantities unaided on the surface, to grow any underground plants at all should require fertilizers of some kind in the very least, and possibly a specialized growing structure for certain more valuable or more tenable crops. (For example, stacks of irrigated wood slabs could be used to grow certain crops for a few years before turning into compost. The compost could then be used as fertilizer for different crops for another season.)
This means you're in a bit of a predicament if you want to make a growing vault. Your fertilizer source has to be steady to produce crops underground for more than a couple seasons. That means heading outside, gathering materials, and bringing them back to the fortress intact. While it's also possible to make relatively safe growing areas for surface flora as well, they would require sunlight - and therefore, openings into your fortress an attacker could potentially exploit.
Of course, there could be exceptions to this. If you come into a mineral source of fertilizer such as nitrate deposits or sunken masses of peat, you might never have to forage outside again. By chipping away at it a tiny bit each season you could keep your farms running for years, even decades if you have a large enough deposit(s) to work with. Another medium-to-low quality fertilizer for certain fungi could be silt from a riverbed. Having access to an underground river in particular would be highly advantageous as it would supply you with a constant flow of silt and water, letting you grow at least some crops underground so long as the river remains safe to use. None the less, to get the most out of your farm and the widest variety of crops, fertilizers should be necessary. (What if certain valued fungus crops grew only on wood or surface flour, for instance? What if silt fertilizers only produced marginal yields of crops, requiring that you make a special effort to keep the fortress alive on that alone?)
Pollution Mechanics That Favor Open Air -
In another recent thread I conveyed my vision of a good pollution system, complete with a temperature-like pollution flow. Without going into nearly so much detail, stagnant air should lose quality quicker and refresh slower. (That is, pockets of air that don't interact with the outside should retain pollution much longer.) While dwarfs could be well adapted to poor air quality, it should still eventually cause problems for them in the form of heightened pollution, leading to unhappy thoughts and higher susceptibility to disease. (For other reasons such as the absence of wind and rain, tiles indoors contaminated with nasty things already linger for a longer span of time, and should pose a greater threat to the general health due to that fact.)
To hamper the spread of disease and keep your fortress healthy, ventilation should be necessary, which again opens you to attack by forcing you to poke holes in your fortress ever so often. The good news is that these ducts would be easy to defend, but the bad news is that if especially formidable or crafty baddies found their way in, you might wind up with an air duct full of sapped traps or worse. Vertical air shafts could become garbage chutes for saboteurs who would then drop payloads into your fortress from above. ("Dorf Dorfington cancels task; interrupted by flesh eating beetle swarm.") Even if your fortress is rock solid, security comes at a price.
Aggressive Cave Adaptation -
A relatively minor suggestion; cave adaptation should produce somewhat more harmful symptoms. Minor decline in eyesight, somewhat heightened vulnerability to disease, minor depression, that sort of thing. While this doesn't have a truly colossal impact on the survivability of your fortress over the short term, over the long term (along with the issue of pollution, hunger, and attackers using contaminants as a weapon) having a fortress full of cave adapted dwarfs would be harmful overall. At best, they're simply somewhat unwell folk going about their business until a good sortie breaks the siege, making it a manageable problem. If you can set aside a protected sunlit place the siege can't attack for everyone to congregate in on a regular basis, the problem won't even exist. On the other hand they could be a plague waiting to happen, which could be very bad if their cave adaptation is aggravating problems already caused by hunger, injuries, and poor sanitation.
Making Sieges More Aggressive -
Siege Engineers -
Military builders and miners that don't act as civilians, can fight, and will continue working under pressure from the enemy. They could build siege works, engineer ways to get into your fortress, or just dig their way in given enough time. The diggers in particular would make guard dogs very useful. ("The war dog is acting strange," followed by, "The war dog senses danger!" An animal trying to alert its owner to the presence of odd noises could move to the spot where noise is being detected. High quantities of vermin could generate occasional false positives.)
Saboteurs -
Sneaky little bastards that behave much like thieves do already, only they actively take stock of your traps, secretly damage them and other pieces of machinery if possible, and leave behind lovely things like noxious smoke bombs and vials of poison for your water supply. Assassins could follow, secretly wreaking havoc on your fortress by going after anyone who looks important with poison darts and crossbows.
Better Siege Engines -
Moving siege towers to send invaders leaping over your walls? Horse-drawn catapult carts? Trolls with battering rams taped to their fists? Yes we can! Giving the catapults better things to fire such as pots of burning tallow, rotting carcasses, and baskets of caltrops would be a nice touch.
Kaiju and Other Creative Ways of Bringing Fortresses to Ruin -
Nothing says 'I want you dead' more than unleashing a giant monster on your opponent's fortress. That Bronze Colossus is a way of telling the world you mean business. Cages full of dangerous animals, swarms of irritating or dangerous insects, and untamed monsters could be dropped into a fortress by the enemy to spread destruction, disease, and general ill will all around. As though they needed to be more aggressive, demons could enlist the aid of imps and other nasty creatures by causing them to appear from nowhere around your fortress from time to time once they've risen from their pits, and could continue to do so until vanquished. You might want to keep those crossbows ready.