The Wii U shop knows what VC games you've already purchased for Wii, because it offers upgrade pricing for most of them. And there are a few games out there that do cross-buy between the Wii U and 3DS shops.
The multiple purchase issue is a strategic/marketing issue, not a technical one.
I suppose this makes sense for the average person, as most people probably don't understand how to use emulators and what not. Oh well.