What I think you are missing here is that all of this can still be true with Zelda still being turned in to a damsel, which is something a lot of her fans hate. I think a lot of players recognized that as soon as Zelda revealed herself she was probably about to be kidnapped. I know I did. The predictability of that event is fed by the prevalence of the trope itself.
The name of the trope as it appears in Ocarina of Time actually has a specific name:
the empowered damsel.
Ocarina of Time shares some similarities with Breath of the Wild in that Zelda is guiding Link on his journey to awaken mighty heroes. She has an active role in the story, drives it forward, and provides the context and motivation for everything Link does. Even though Link is the hero, his adventure would not be possible without Zelda. Zelda, as Sheik, is also highly skilled in stealth and deception. She is a badass. She is, in my opinion, an unrivaled supporting character as far as the Zelda series is concerned. Zelda's growth as a young-girl-with-a-plan in to magical ninja orchestrating her own return to power is truly excellent and pretty ahead of it's time for 1998.
Zelda is portrayed throughout the game as a mastermind. She is ahead of the game. At any given time, from the moment you meet her, she knows more about what's going on than anyone else. She devises a plan, puts it in to action, and improvises on the spot to ensure her longterm success. As an adult, she has excellent survival skills and physical prowess. She has skills Link does not understand. She has knowledge Link can barely comprehend. She is a ninja. She is a musician. She is a historian. She is a leader.
All of this rules.
However, despite all of this, Zelda
still becomes a last-minute damsel in the most classical and traditional sense. This isn't really a question. It's a codified and exemplary demonstration of the trope. Ocarina of Time portrays Zelda's survivor identity as a temporary necessity. It only exists until she needs to be kidnapped for story reasons. Then it's back to tradition.
Why does Zelda, the Sheikah ninja, after a lifelong effort of careful deception and disguise, transform in to a pretty pink princess in the extremely vulnerable Temple of Time? Well, it's because she is about to be kidnapped to add more stakes to the narrative. Now, not only is the mission to defeat Ganon, it's to rescue Princess Zelda. You don't get much more "damsel" than a pink princess imprisoned in a crystal. She sheds her strengths, her powers, and puts herself in to a risky position strictly so the story can move her from actor to object. This is a real pity.
It's not all bad. While her role is mostly passive after her transformation, she does restrain Ganon with her magic in the final fight and is able to open the barred doors for she and Link to escape. But she still becomes all chest-clutchy and gaspy at the sight of all the falling rocks and takes no part in dispatching the enemies as you escape. At least she doesn't need to be carried out of the castle fireman style or something. But her entire personality and demeanor changes dramatically, as do her apparent powers and skills, after she puts the dress on. Much of this can also be said about Tetra in Wind Waker, which carries out very similarly. The baby step made in that game is that Zelda uses the Light Arrows in the final fight. This sort of tiny, incremental progress isn't super satisfying after two decades.
The empowered damsel is like a half-step towards full female narrative dignity. It's certainly better than a passive damsel with zero personality or narrative influence - a literal retrieval object (which Zelda
has been in the past). But it's just bettering a common trope and relying on it to create drama for male characters. Given how old Ocarina of Time is at this point, I don't think it's unreasonable to hope future games are able to break the damsel tradition entirely.
Zelda is still damseled. She's just a more empowered damsel than usual. Not all damsels are created equally, you know? It's not a trope that exists in any one, singular form and not all of its depictions are equally bad. You might even feel like the trope is used
effectively, but it doesn't mean the trope isn't present. Regardless of how you feel personally, you can probably understand why it's disheartening for many to have such a cool character revealed to be Princess Zelda only for her to immediately be kidnapped and need to be rescued. It's as if to say her true identity, and true place, will always be in Ganon's clutches and waiting for Link to save her.
But now we have this thread which is 100% going to make Zelda playable, finally. So that's good news.