I'm fairly sure this has to do with the contractual rights and/or royalties involved to sell virtual console games rather than anything to do with space constraints.
There was a really good episode of Retronauts where they explained why it was so difficult to for companies to put retro games out there on platforms like VC or XBLA - a good example they gave was a movie game like Batman for the Sega Genesis, where they not only have to give royalties to publishers and producers but also the movie studio who owns the rights to the Batman franchise, DC Comics, etc - everyone gets a cut and a lot of times the $5 price tag doesn't cover the meager sales the title might generate. I wouldn't be surprised if some of the more obscure games sell in in the single digits some weeks, or even less.