This article says the car was found in the aft of the hangar:

https://www.theautopian.com/a-ford-woody-wagon-was-found-aboard-the-sunken-wwii-aircraft-carrier-uss-yorktown-and-no-one-is-sure-why/

This Navsource photo shows the aft of the hangar on June 4th:

https://www.navsource.org/archives/02/020513.jpg

No car.

Caption reads:

"Scene in the hangar of USS Yorktown (CV-5), 4 June 1942, shortly after fires there from Japanese bomb hits had been extinguished. This rather fuzzy time exposure looks directly aft, with the sloping inner uptake sides at left. One bomb, which detonated on the flight deck just aft of the midships aircraft elevator, set fires in the area seen in the left distance. Note fire hoses on deck, and spare TBD-1 "Devastator" torpedo plane (with obsolete markings) hung under the hangar overhead.

Official U.S. Navy Photograph, now in the collections of the National Archives (photo # 80-G-312023)."

Ship was abandoned June 4th. Most of the major jettisoning took place on June 6th, and took hours. It was still ongoing when the torpedoes hit.

Accounts:

https://www.navsource.org/archives/02/020590.pdf

http://www.cv5yorktown.com/Documents/Reports/Loss/

https://www.history.navy.mil/research/archives/digital-exhibits-highlights/action-reports/wwii-battle-of-midway/uss-yorktown-action-report.html

The car was almost certainly stowed below somewhere, not on the hangar deck (and could even have been drained of gasoline to reduce fire hazard.) The salvage party aboard on June 6th at some point figured out it was another thing they could jettison. It would possibly not have been easy getting it up to the hangar deck from the hold below. I am not sure what elevators were working, and without gasoline, it would need to be pushed around to boot. If my theory is correct, and it was stowed this way, it was not the first thing on anyone's list to jettison. From the accounts above, you can see what had priority. They had not even got all the spare planes down from the hangar overhead when the torpedoes hit.

I don't read plans well at all, but it looks to me like most of the access to the holds for the hangar are aft:

https://maritime.org/doc/plans/cv5.pdf

My theory is that the car was stowed below, manhandled up to the aft of the hangar, then the torpedoes hit, and jettisoning stopped, and the ship was reabandoned for the last time. I think another half hour at most before the torpedoes, and no one would have found that car there.

My two cents.