By the time the flight deck AA guns were installed, Junyo was mainly being used as an aircraft transport. I don't think she launched another aircraft from her flight deck after being damaged at Philippine Sea.
Another possibility might be that the single 25mm machine guns on the flight deck were dismountable mounts, i've got that impression because their placement is outlined with a darker shade on the flight deck.
Ibuki (my everlasting CV project
), for example, featured a foldable Type 21 radar right in the middle of the flight deck, just forward of the bow elevator.