Nintendo was against CDs at the time for 3 main reasons:
1. Increased cost. Iirc, it launched at $199 here in the US and double speed CD drives at the time were $100+ dollars even at it's launch. They likely could have done $249 at a loss, or more likely $300 without a loss as Nintendo likes to make money on the hardware that they sell.
2. CD access time. Miyamoto and quite a few others are on record saying that it killed the game experience in their view, at least, with double speed drives.
3. Piracy!
I'm sure there are other points but those are the main ones. Piracy seems to have been their biggest concern really, it's even why they went with mini-Dvds on the Gamecube, and those discs spun in reverse vs every other drive + there was heavy encryption on top of everything else.
A zip drive like the 64DD with it's unique discs, now, maybe Nintendo would have done that at launch if they looked at it early enough. I think that would have made the games much cheaper than carts but still not as cheap as CDs, would have fast access time [slower than cart but MUCH faster than CD], and if designed right, would be very hard for pirates to harm their bottom line. The 64DD disks were 64MB vs the launch carts being 8MB. They could have found a way to up that to 256MB for it's zip disks if they went that route most likely. That would have been interesting if Nintendo went this route instead of carts.
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