The other thing to consider is market. I highly doubt Nintendo thinks tweens are going to buy GB games; they're for older people who loved the games and want to play them again, or missed out on some and want to play them for the first time.
Sure there might be some younger folk who love Zelda, want to play them all, and don't have emulators, but they're so few Nintendo can' count on them for revenue in the 3DS VC.
Us "older" gamers, who are more likely to have disposable income, and more likely to buy these game, would also be more willing to pay $3-4 for GB games, $5-6 for GBC games, and $7-8 for GBA.
Sure that's a little expensive, but how many of these games are you really going to buy? Spending $8 for 3 or 4 worthy GBA isn't that outrageous, and it's basically free money for Nintendo.
Just a side note: AMC sucks because it has commercials. They can call the channel whatever they want, but people much prefer to watch TCM (which shows a ton of B&W films) and FMC because they don't have commercials.