I figure they think it would eat into sales of re-releases or just wouldn't appeal to a big enough market. Nintendo is very much into big mainstream hits so some fringe product that appeals to geeks does not seem like it would be on their radar. Someone like Reggie probably has no idea about any retro videogame scene at all. The funny thing is that someone is making money of off systems like the Retro Duo and replacement SNES controllers and replacement NES cartridge connectors. There clearly is SOME market and, if not embarassingly overpriced, an official Nintendo version of that stuff would probably squash the third party stuff. If you were interested in a Retro Duo and a new legitimate Nintendo version of that product existed isn't that the one you would get? Let's not ignore the used game systems that sell on eBay that Nintendo currently gets $0 from. The products exist and someone is buying them and Nintendo doesn't make a dime off any of it.
The ironic thing is re-releases led me to pick up at least 3 systems and at least a hundred games of the past. I started buying VC games, then realized Nintendo would never release them fast enough and they would never release many of the games I want to play. I think they could make $100 million easy on it, but they'd have to use the Disney re-release approach. Release a limited amount, like 2 million NES systems, add some cool collector packaging, and then people would scoop them up. Since the NES is so cheap they could probably make a profit of $40-50 an NES which would add up to $80-$100 million on hardware. Then re-release about 20 games from the era at a price of $20 could add to the profit. They could also encourage 3rd parties such as Konami to rerelease say Contra and make even more $. The key would be to keep it limited, so the NES systems sell out quickly and it doesn't really affect current console demand. Then you re-release a SNES in 5 years, etc, keeping the re-releases limited.
Most of the games, I'd re-release are so popular they probably wouldn't even affect re-releases. By that I mean, most people that would actually buy a VC release of Super Mario 3 probably already own a version of that game for some system. Embarrassingly, I have Super Mario 3 for NES, GBA, Super Nintendo, Wii x2(I bought the digital version and disc release). I don't think I'd buy it again for Wii U, but I'd strongly consider it for the 3ds if they released a digital version. People like to play these games on new systems and generally the price isn't too prohibitive to re-buy.