Nintendo has many male protagonists
Regardless of if their other series are improving (3d world + movie makes me think Peach's days as a damsel may be outnumbered, and the Odyssey ending is arguably progressive in some way though it was kinda weirdly toned compared to typical Mario) or not (Kirby generally has 4 playable characters now and all are guys, I don't wanna scrap any of them but do wonder if someone else could be added, I'd say Tiff tbh but they don't want the anime to be that connected I assume), there is one thing in common
These are very defined characters. We play as Mario or Kirby or whoever, and to the extent any game character is, they are analogous to the player. But they are still primarily their own characters. Mario is Mario above all else.
Link is to some degree, an avatar. For a long time you've been able to name him. There has been an insistence upon the inability to speak because he is meant to be a shell. Well he has more of a direct story role then say, a Pokemon Trainer (in terms of lore stuff, I suppose beating the evil team is major too), he is primarily an empty slate that has some backstory.
Despite Aunoma believing otherwise, I do not believe Link's gender is integral to his character in anyway, considering how much vagueness there is surrounding him. Most other games with an avatar-esc character do let you choose, like going back to Pokemon it was always the plan, it didn't happen at first cause of technological limits but it came soon enough.
Letting Mario be a girl, while largely inoffensive, would be a bit weird cause Mario is such a defined character. Link, while iconic, is not only open ended but has many versions, in every Mario game besides maybe Paper Mario its the same guy. Perhaps the canon is weirder with hints of them being actors in Mario 3 and such, but its not some multiverse at all. Even the Paper thing is a modern era retcon that the RPG era PM fans hate.
Meanwhile with this game and like 3 other exceptions, every Link is his own. So the idea of choosing male or female feels very obvious, yet again, Aunoma seems to believe it goes against Link's character on some fundamental level.
If that is the case, then fans will naturally shift to the most primary female character, who can best fill this role. I do believe the primary goal is just a female protagonist, as there was little Zelda talk until after rumors- followed by a denail of - of female Link in BOTW.
Whether it will ever happen I don't know, perhaps if leadership changes, then again Peach seems to not be directly tied to leadership considering what Miyamoto said about her in the movie, perhaps its just whatever suits what situation best (aka if the game has 4 player multiplayer from now on Peach isn't captured, but I'd hope the next 3d has multiple playable characters and Peach is one, though avoiding a DK64 situation may be hard)
Usually when Nintendo is refered to as a "conservative company" we are meaning resistance to industry changes, resistance to bucking their own trends which, ironically can be the opposite of conservative (as in they are conservative by refusing to stop innovating in wacky ways), but on some level they are on a social level. I believe it is a lot better then it could be and has been getting better in recent years, both EPD 5 and 9 seem to be doing great in that area I'd say, as well as GameFreak, though for EPD its harder to really implement in mario kart perhaps. And this was very much good news:
https://www.engadget.com/nintendo-japan-same-sex-marriage-benefits-175653064.html. And gives me hope that the (imo inevitable) Tomadachi Life Switch will deliver on that old promise (you could argue Miitopia did, but the relationships in that game are a lot less explicitly romantic, it feels like it can thread the needle). But they are still a Japanese company with primarily fairly old leadership, and in many cases the essentialization of gameplay, intentionally or not, makes a good excuse to avoid these changes.
Despite this, as many in this community are aware, there are many fans who are not of the most stereotypical "gamer" groups, regardless of how much of a bubble the places I'm in are or are not, I do think it's fair to say there are many nintendo fans of color, who are women, who are members of the LGBT community, who desire more clear representation. Their protagonists are predominantly male, and the human ones predominantly white or at the least very light skinned. Zelda, being such a big series and one with some idea of representing the player, is one that many would love to see themselves in, and if Link cannot be molded to fit players who want to play as a girl, then playing as the leading woman is the next best thing.