You don't need any ventilation. Dwarves can breath even if they've been in a hermetically-sealed steel chamber a hundred levels underground that completely submerged in magma that is, itself, in a hermetically-sealed steel chamber that is completely submerged in water for a decade.
No, the cause of your dwarves suffocating is more sinister. There's 2 possibilities. The first, and less likely of the two, is that your suffocated dwarves were injured in such a way that their lungs no longer functioned, such as by having their lungs destroyed or their spines severed. This is unlikely because you'd probably notice such a thing occurring, and it's usually quick, too.
More likely is that you killed a forgotten beast, titan, or other randomly-generated creature that had deadly dust, deadly blood, noxious secretions, or possibly other special properties. These things cause syndromes to those affected by them, and these syndromes can include shutting down of organs, including lungs, can occur some time after contact with the substance that causes them, and the substance that causes them can continue to exist and cause syndromes indefinitely after their creation. You should set up a dwarf bath, get DFHack and run DFCleanMap or otherwise find the beast's blood or extract and remove it (magma is the best way), and clear your fort of deadly substances.