Hmm, yeah, that sounds odd. If it only happens with Zelda it could be a rogue disc or something, though that's the only thing I can think of. My GC is sitting on my DVD player and I've had some four hour plus long sessions and it hasn't frozen once.
Mine froze in the bird village as I was exiting a room. GC is on a wire shelf and has plenty of ventilation. Luckily I had saved about 30 seconds before(after not saving for 2 hours), so I didn't lose anything.
I've noticed that my Xbox makes a certain noise right before a DDE(the disc suddenly stops, then the drive spins up really fast), and when I heard the cube make a similar noise, my heart almost stopped and I saved immediately.
I was having a problem with the Cube locking up on Metroid Prime, about 5 seconds before it locks up I heard a clicking sound, then it locks. So, to stop the game from locking, as soon as I heard that sound, I'd open the disc cover. The GameCube will tell you to close the lid and the game will pick right back up where it was. Just my 2 cents.