The old man and baby survived because their bodies' pH wasn't normal. But pH can be affected by a lot of health conditions, including such mundane things as being on a diet. Were there no diabetics in the entire town? No bulimic teens? Nobody who started to hyperventilate when they looked out their window and saw some of the neighbors keel over in the street?
It didn't kill everyone immediately... some of them went 'quietly nuts' and committed suicide when they saw what had happened to their neighbours.
It's also implied that those who did survive long enough to fall into this latter group might have been mildly acidotic due to disease, as OP states; just not enough so to survive entirely. Peter Jackson mentions that the "doughboy" was a poorly controlled diabetic who "hated the needles." The old lady has a pile of cigarette butts in an ashtray, implying emphysema if not COPD. Both will cause varying degrees of acidosis.
Also, blood pH in humans is both A) self-correcting, and B) exists in a range rather than a discrete number (7.35 - 7.45). People on restrictive diets or with respiratory problems generally compensate - i.e. alter their circulating levels of either carbon dioxide (present in blood as carbonic acid) or bicarbonate - within minutes to days of a pH shift outside the normal range. (Look up "arterial blood gas interpretation" if you'd like the full details.) A hyperventilating adult will stop hyperventilating eventually, at which point the pH re-regulates and he/she is Andromeda bait. The baby survived because all he could do was cry, thus remaining alkalotic enough to stave off Andromeda. It's true that a diabetic currently in ketoacidotic or hyperosmolar hyperglycemic nonketotic states would survive an Andromeda exposure, but that individual would likely have died of their diabetes in very short order - they'd still be dead with everyone else, just not dead of Andromeda.
All the rubber and plastic, etc on the crashed airplane was gone, but there's a landing gear with a tire sticking out of the wreckage.
At the crash site, one of the techs mentions that there was no rubber on the plane, just a plastic called "Poly-Cron," which was consumed by the Andromeda bug. The tire, which the tech probably didn't think of as "on the plane," was made of ordinary rubber.
The big heart-stopping finale is solely due to the fact that Wildfire (which had been in operation for months) was set to blow up unless the nuke-deactivating key was inserted before the time ran out, but the deactivation terminals weren't all installed yet. Wouldn't that be considered remotely important?
While the facility has been operational for a while, it wasn't in full use until the events of the book. Since at least some of the terminals were functional, it was assumed that they could shove installing the rest to a lower priority. They thought they had much more time than they did.
The nuke is meant to prevent an accidental release of a horrible microbe. The deactivation key is only included so that one of the scientists intimately involved with the project can stop the process if he deems it necessary for some reason. The most likely scenario by far would be to prevent a false alarm from destroying the base. If a false alarm did end up destroying the base, then it would be a regrettable loss of life and property, of course, but the wider world would continue. In this case, the reason to stop the bomb is because Andromeda feeds off of pure radiation, so an atomic blast would not only fail to destroy it, but accelerate its growth and mutations. This is an entirely unforeseeable complication for the designers and builders of Wildfire, so while in this particular situation the absence of deactivation stations is world-threatening, generally speaking it wouldn't be an issue, especially since the chances of anyone needing to deactivate the self-destruct before construction of the base is even complete is One In A Million.
OP is also forgetting that this is a staple of all of Crichton's works: the fallibility of man in regards to technology. From this to Jurassic Park, everyone believes that they've taken all the precautions needed and "the worst case" simply WON'T happen. In this case, Stone and the rest had absolute faith that they'd built the perfect laboratory to contain any microorganism encountered. From Poly Cron gaskets to the glove box rooms to all the biochemical barriers and decontamination procedures... Nobody ever thought that the "last resort" would actually have to be used, hence why there were fewer than ideal number of stations when initially designed.