Yep, that's the reason for why Smash Wii U underperformed in Japan. 3DS version cannibalized considerable sales from the Wii U version. If Wii U version was avaliable first, it would sell better and even boost hardware sales as well. 3DS version coming first destroyed that. Yep, some will say this was a "smart move" and sold a lot on 3DS, and Wii U is a "dead system", but eventually, compromised one of the biggest prospects for hardware sales on Wii U.
Splatoon being Wii U exclusive is a major reason for why the system got some attention in Japan at the moment. A 3DS version, if was made, would took any attention from Wii U, like what happened with Smash Bros.
Smash U as an Exclusive wouldn't have done jack for Wii U hardware.
6+ million (what's the latest Smash 3DS number anyway) sales on the 3DS is worth far more than any benefits the Wii U would have seen.