Will it impact sales? Of course, I mean you'd be in denial if you thought otherwise.
Not everyone is a super big fan of the series like quite a few here on this forum, in fact, I'd wager the majority of purchases will be made from gamers looking for a casual fun experience on either the Wii U or 3DS. So let's say you own both, and given what I said about the main audience who is going to buy this game, would you actually buy both versions? The answer in a lot of cases would probably be no. Both are being marketed as the same game only on different platforms, which, essentially, is what it is. A part from the odd exclusive perk here and there, maybe an exclusive stage/mode/character, they're practically the same game only running on different sets of hardware. The Wii U will be seen as the complete living room experience for the family and regulars of the franchise, while the 3DS will be seen as the more mobile, on the go type of experience - throw in the novelty that this is the first handheld installment in the series and it matches well to its big brother counterpart.
So really you have two, nearly identical, games which begs the question, why buy both? Not everyone can spend that type of money or would even be willing to buy two games that are virtually the same. Though this works both ways, some will possibly skip out on the 3DS version and wait for the Wii U version (might be personal preference of preferring home consoles). So you could have a case where both game sales are effected to some degree; however overall sales will show a pretty good number there's no doubt in that.
Here's my problem though, the Wii U isn't doing too good, and despite the sugar coating that people give it, it needs sales and fast. SSB being one of the console's main juggernauts--in terms of sales and mainstream attention--is vital. So with these two versions, will people opt out of potentially buying a Wii U, stick to their 3DS (numbers show that this is by far the most popular product) and not buy a Wii U because they can already experience the game? I'm damn sure this is the case for a lot of people who are still on the fence about buying a Wii U, so the best option, financially and logically, would probably be to stick to the 3DS and rather than spending an extra £250 to get the same game you've been waiting for.