Then again, every spacecraft has vents leading directly outside - they are called walls.
Some of those are capable of holding against up to one atmosphere of pressure. If the creature exerts more, it pushes through, though. Not all vents need be armored against extreme penetrative force - but OTOH many would benefit from being permeable to some overpressure. And we learn that the creature can indeed push through stuff: the shields of the ship, or the jar holding the blood bait...
What concerns me more is that the piping that carries radioactive stuff inside the impulse engines connects directly, by design, to the cabin ventilation system. What is the functional need for this cross-connection? It sure comes in handy in this adventure, of course!
As for the "home" bit, it's iffy at best. If this creature is capable of star travel and of breeding, then there only existing a single individual at a single location is extremely unlikely. If and when it's a whole species, then the planetoid might be a preferred breeding (splitting!) grounds, and other individuals would come to breed/split at other times. But they would in all likelihood also find other planetoids to their liking. Perhaps Kirk, even if "tuned in" by his previous encounter somehow, misread the scent?
Perhaps breeding requires a blood feast (as with mosquitoes, say), and a breeding planetoid is defined by lacking one and thus offering maximal peace (as with all those birds that fly to the barren north to nest)? Might be an individual feasted and then bred eleven years prior to this episodend then one of its offspring feasted and withdrew to breed during the episode? To a dilettante like Kirk, all gaseous clouds would look alike anyway...
Such a short generation would probably imply trillions of individuals within the UFP alone. Perhaps few are as ill-equipped to deal with hunters (generally by hiding), and Kirk here downed an already wounded or otherwise disadvantaged individual?
The scent thing in general makes sense: if these individuals are ill defined, in having a fuzzy boundary, then Kirk might well have inhaled a certain percentage of the creature, and would be carrying bits of its consciousness within, the creature itself being little affected by this. But there might be a longing there, too, the cloud wanting to reabsorb what Kirk once inhaled. Perhaps that's what "home" meant? That soon the part within Kirk would be back home, thanks to the mother cloud's devious plan of luring the starship to empty space far away from help, then turning around and attacking - a course of action that makes no sense otherwise.
Timo Saloniemi
can travel at warp speed without being inside a spaceship. 
As a related aside, I don't think it's clear that Kirk was the only survivor on the Farragut (not that you implied that - just musing aloud, as it were). 
