As far as Konami goes, I don't think their problems are necessarily handheld-centric.
Same with Capcom. Yes at the start of the gen, there was Resident Evil as well, but outside of that, nothing's really changed from last gen outside of killing Mega Man.
Sega's still trucking on Vita with Phantasy Star and Project Diva.
These aren't the types of titles that would likely find too much success on mobile.
Capcom I view more as interesting from the perspective that they started with Street Fighter, Resident Evil, and that mystery adventure game, then tried things like E.X Troopers, and now they look poised to pretty much reduce to just Monster Hunter and Ace Attorney, their safe handheld hits from last gen.
To me a handheld to mobile shift is not about every last game disappearing, it's about the volume steadily shrinking down to primarily the biggest hits a company has, with investments in new titles and revived brands being made elsewhere.
Like Monster Hunter and Ace Attorney are really obvious fits for the 4DS. Will they bring anything else? That's more the kind of questions I ask and the kind I think Nintendo should really try to get publishers to answer with "Yes."
If those titles are cross-platform with mobile, they're at least still on 4DS, even if that does give people other platform options for playing them.
It's like how Sony and Microsoft had a notable issue with indies toward the end of last generation as they were walking off consoles and going to PC and mobile where they had significantly more success. The platform holders made major policy changes and worked with the technology providers who powered indie games, and now they're coming back.
Similarly they tried to bring back developers who went into free 2 play by making that far more workable.