Because when you dive in the water you begin to lose health which the game views the same as air, and when you surface you regain "air". In later Mario games it has separate meters for air and health, however this game would be unbalanced if you lost most of your health underwater and then came up with only one bar.
It's just one of those weird quirks that a developer doesn't really think to fix until after the game has already been released. In hindsight, Nintendo probably agrees with you that it would have been logical to have a separate meter for oxygen.
hmm, IDK just the way it was lol, remember mario was the first 3D platformer ever (to my knowledge) so there were a lot of things that it had that were evolved today. (most of which were evolvedin the banjo kazooie games by Rare.)
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