The Link-Zelda ship problem is that all Zeldas are each other’s blood daughters, and all Links are the same “soul of the hero” despite being different people. So they don’t want to have any incest story baked in this reincarnation stuff, and it stays platonic most of the time. This was a retcon (kinda) introduced Skyward Sword, probably to justify why they’d been avoiding it the whole time, previous games like LttP and OoT would only say that the various Links were just from some royal knight families or “the last of the families of knights”.

Skyward Sword is the very first incarnation of both of these characters (Zelda being the first human incarnation of Hylia, and we don’t know about Link), so they can be in love - it goes out of focus, but it’s assumed to still be there at the end. And then BotW is the very end of the timeline, tens of thousands of years later, so that’s fine, they’re very clearly in love there by the end, and live together in TotK.

There’s also some hints in the Wind Water timeline (I think in Spirit Tracks but I never played it), because that timeline insists that this is a new hero unrelated to the previous soul of the hero.