I always liked the notion that they didn't go to just one place, that they were more "on the run" than "hiding". If they did hide, it'd only be for long enough for Impa to start disguising and training Zelda.
Anyway, I also wanted to make a quick little comment on the issue of the map and Hyrule's geography changing. I do think Hyrule is larger than we see in Ocarina of Time, but I think it's something we mostly have to suspend our disbelief with because it comes down to hardware technicalities and capabilities. I think after Ocarina of Time rather than seeing new areas north and south of what we saw before, the land simply got larger and locations spread out more, because the systems could handle more.
The reason I say this is because the maps do actually look very similar, if you look at them from different angles. It obviously doesn't all add up perfectly, but it's worth noting, I think.
I tried to turn that
ALttP one so that Faron was at the bottom and it was diamond shaped, but I couldn't get it right, so tilt your head a little with that one.
From there, all sorts of interesting theories can come into play. Maybe Lake Flora of
SS goes onto become Zora's Domain of
OoT, with the forest getting cut back somewhat as civilizations grow. And then maybe even after the unfreezing of Zora's Domain, things never quite work out, so they leave and make a new Zora's Domain up in Lanaryu. Obviously Hyrule Castle gets relocated to the center of Hyrule sometime after
OoT, and so on.
Again, it's not perfect, and I'm sure this has been suggested by people before. But reading this thread, I felt like suggesting it. This is my first post, after all.