Y'know, I think you might be on to something, whether you intended it or not...
Observing this argument from a distance, I can safely say there's an important question nobody's answering (but it's been asked a bunch of times): How much does it really matter?
Link's gender doesn't play a significant role in the story (except, potentially, for the sake of bearing future Heroes of Time - but that effectively takes place outside of the game, hence it's not a part of the game's story for the time being). The only reason it matters is they can't risk him losing his iconic-ness - we all identify him as the tall, slender elf-guy clad in green. Introducing full character customization would kill the franchise outright. Picking a gender (I particularly like Linkle's design, even if her name is rather uninspired) should be possible in a perfect world, but sadly we don't have that - we instead have a
financially significant number of entitled fans who might react negatively, and while there's absolutely no defending their behavior, the problem is it's bad business to tick them off. Hence, we have a gap - and I'd put money down that the developers have not only identified it, but have already been putting a solution into place.
What do you notice about Link's design with each new iteration?
We see him becoming more and more
androgynous. This is critically important to the claim that Link is literally the link between player and character! The designers want you to associate with this character, whether you're male or female, so his design draws attention away from the fact that he's a man. He's not some buff macho-man like Kratos or Nathan Drake - he's a tall, slender, skinny dude whose appearance is as far from threatening as you can get.
Sadly, I can find no source that says this outright, but to me, it's evident that the problem is clear in the developers' minds. Were he not an iconic character, there'd be a simple solution, but in his case, it's not as cut and dry. What we have instead is a patch, one that gets a little better with each iteration. Is it a perfect solution? No. But at least they're trying.