Well Zelda's loading times aren't hidden in the dungeons. Often I'll run through a door, the screen fades white for ~2 seconds, then the next room pops up. The same thing happens on Outset Island when going in and out of huts. On the old cartridge version of Ocarina these transitions were instant... no loading time required.
re: Super Metroid. I was playing this old cartridge game yesterday, and I noticed it has lots 10 second elevator transitions. Also, I had to shoot a lot of doors. Are these hidden loading times too? (Just kidding!) But seriously, I think the elevator transitions/door shootings are there in GameCube's Metroid, because it was in older versions. It's part of the series "style". The programmers probably could have eliminated the doors/elevators if they wanted.
Why'd I ask this question? Just curious. I'm an engineer, so I want to know how things work. :-)