Concidence, the writers craft the story, the director has zero influence on that front.
I'm loving all of the responses.
When writing the OP, I started to wonder if it was because of the dark matter asteroid they "power of math'd" into the shuttlebay.
I would think repairing a big vulnerability like that would be at the top of the repair list.
Then again it could all be a rouse, similar to the holo masking technology Georgiou wore. The bay doors are camouflaged.
Pike wants you to think you can just fly on in.
Then Bam! Splat! Send Ensign Ricky to clean up/ scrape off the mess.
It is most logical.
Actually, I think Star Fleet never imagined a situation (beyond total destruction) in which the ship would need a spare.
These two elements just might actually fit together. For all we know, the Crossfield class was partially based on a largely-hollow shuttle carrier spaceframe, as fandom sources had long interpreted the original Planet Of The Titans concept art which inspired its design.
Not necessarily all the time. We only hear of it explicitly on a handful of occasions. And a century later on Voyager, Janeway would still sometimes order the very same same launch procedure to be followed—"depressurize the shuttle bay and open the space doors"—even though they were shown to also be capable of launching TNG-style through the force field with a pressurized bay at others. Two examples of the former that spring to mind are "Threshold" (VGR) and "Innocence" (VGR).
She definitely has physical doors, even though we seldom observe them in use. They are seen each episode in the opening credits, and were occasionally shown closed in the first season, such as in "The Butcher's Knife Cares Not For The Lamb's Cry" (DSC):
On the Enterprise-B/Lakota variant at least, that lower bay is filled with apparatus that doesn't really suggest a hangar deck. As for the upper stern fantail, according to Drexler's MSD from Generations, it's a cargo bay in that iteration. (Of course, if one goes by that, the shuttle bays are located inside the additional saucer impulse engines!
)
-MMoM
