The scene of the seaplane getting shot down was from a made-for-TV addendum to the movie that fleshed out the Coral Sea battle in much more detail. I wish they’d make that version available as a bonus feature on DVD because I’d like to watch it again. It’s been years since I’ve seen it, but I remember liking the fictional pilot (a family friend of Admiral Nagumo) and being saddened when he got shot down.
Found the footage on youtube: “Emily” Jap flying boat being shot down. Also known as the Kawanishi H2K8, similar in size to the Boeing Clipper 314. Unlike the Boeing 314, there is a surviving Kawanishi.