Oh absolutely, just look at how long poor Yokai Watch 4 and the HD Inazuma Eleven games have been delayed. And on the other side of the ticket, poor Compile Heart looks absolutely lost without the Vita to sell its low budget fanservicy RPGs. Its latest release "Arc of Alchemist" sold just 3,300 copies last week (its initial week) in Japan. That's not a port. That's a new retail release.
There certainly are handheld developers that can make that transition fine, but there is no doubt in my mind that there will be many hurt by the loss of 3DS/Vita development. And I believe that transition is why numerous Nintendo Switch games (Fire Emblem being the latest one) have gotten delayed, sometimes several times even.