The expense was probably quite considerable. Not only do you have to have the game ROM on a chip, you would also need Nintendo's lockout chip too. If your game had a battery save system (DKC did) you would also need to buy a RAM chip and watch battery too. That's ignoring any enhancement chips as DKC didn't use any (but many other late generation games did).
And all that before you get to the fact that the only who could officially make these boards was Nintendo. Meaning there isn't exactly much competition driving prices down. Sure, Nintendo couldn't quite take the piss the way they could in the NES days, as Sega was all too eager to try and attract new games for its console, but unless you wanted to completely remake your game, you're dealing with the big N's bullshit.
The boards could probably have been made much cheaper today than in the 90s, as ROM memory was expensive AF, even the couple-of-MB ones used in the consoles of the day.
There's a reason PS1 and Saturn games were massively cheaper to buy than N64 games.