No, you don't get it at all. Like, at all.
That people liked these characters doesn't mean anything. It just means he's good enough at writing other aspects of their characters to be engaging (though I'd argue that it's more that he writes the story around these characters rather than that these characters are interesting in and of themselves, for the most part, but that's just me). To use myself as an example, I fucking LOVE the Princess Bride, but I'm not going to pretend that it Princess Buttercup isn't a stereotypical damsel in distress for the male hero to save. It's still a good movie, but that doesn't change that it's adhering to shitty stereotypes.
But sexual objectifying isn't a thing you just make up for. You don't get to get away with sexual objectification just because you do other stuff. That's not how the world works, you don't get to steal something just because you paid like you were supposed to the past 50 times.
The fact that Kojima seems legitimately incapable of writing a female character, even a child, who is not sexually objectified is a legitimate problem both for him and the world view that his art brings to his audience. It's harmful, and he doesn't get out of that because "Well, people like them, so it's okay".
You remember that quote from the final fantasy 15 guy about how he didn't understand why people wanted female characters if they were going to get mad about their sexual objectification? He may have said it, but Kojima is living that philosophy. If he seriously can't write a female character who isn't sexually objectified no matter what, then it kind of implies the value he holds on women. Not that he doesn't value women, but that he primarily values them for titillation rather than as people. And any time you dehumanize people for their physical attributes, that's bad.