No it wouldn't. Going third party doesn't mean not making hardware anymore.
3 ways Nintendo can go third party while still having new releases on their hardware
1) Old classics on ios, android ect. Pokemon blue on ipad is not going to stop anyone that wants a 3DS from getting one. In fact it reopens the market considerably, for those wanting the newest and latest pokemon for instance.
2) Release their less huge/blockbuster games on XB1/PS4/PC. Few WiiU games seem to be designed around the gamepad, so porting would be fine (that said Nintendo would need to bring in people that know how as it's brand new architecture) but for instance DK Tropical Freeze has pretty much exhausted its hardware selling power now (if it had any) so if they could sell 500k - 1m more copies across XB1 and PS4 that would be huge.
3) Put their IP up for auction, highest bidder. What I mean by this is, if say MS wanted Super Mario 3DLand, not only could Nintendo demand a fee for it, but get a higher cut of royalties.
With the 3DS they're better off keeping that stuff exclusive and porting the old stuff to mobile, but WiiU is hardly going to sell any worse than it currently is so they don't have much to lose porting off 2 year old games.
