Well it's totally possible that the problem only occurs with certain discs and you happen to have one that works perfectly. It's also possible that you have a defective disc but it just hasn't happened to freeze on you yet. I know for certain that the freezing glitch is real though (meaning not only due to disc damage) because I received my collector's edition in the original offer and it has never worked perfectly.
Mine would freeze on me now and then. I think its actually great if you can beat the game on the disc becasue the freezing adds a challenge to the game. I had to redo many dungeons because of the freeze glitch. I got it on wii VC instead (well because it was free through club nintendo) so I wouldnt worry about freeze glitch. Also on wii vc then you dont needto worry about gamecube memory card.
It's nothing to do with the condition of the disc, it's an in-game bug that freezes the game randomly and unexpectingly. Because this only occurs when playing Majora's Mask, The problem points towards a porting bug. If you haven't encountered this bug yet, then you've been lucky.
It's on all the discs, they just put to much on 1 disc and because Majora's Mask was last it got the bug. The game is very slow at first, you need to wait for it to warm up once you start. If you push it to far to fast then you will have a better chance of it freezing (like if you speed run from room to room really fast then it will freeze). I remember when I was playing the Great Bay Temple, I was speeding through it and I noticed it was going slower, so then when I opened a chest..it froze. I know now to be more careful and the game works just fine. As long as you don't rush through the game on the Collector's Edition you'll be fine.
Also I got it used from Gamestop in one of those yellow cases 3 years ago, so it's not with the disc. I also have the VC version but I prefer the CE version.