It's either that, or 30FPS gameplay. Something has to give with UE sometimes.
Well that or they could have not used as many of the UE4 post processing and lighting features. Yoshi is a rather advanced game in those areas for the Switch.
As for the larger question, most of Nintendo's internal studios seem to be doing quite well with their own tech. Mario Odyssey and BotW bring in a lot of current gen rendering and post processing techniques with greater efficiency overall than a standard third party engine would without modification. The Mario Kart team has done really strong work in the past with 8 and also on Switch with Arms, I would trust them to advance things on their own. Monolith Soft had some bumps with the Xenoblade 2 engine but smoothed a lot of that over already with the Torna iteration. I doubt they could get much better results from UE4 and there are some proprietary tricks on display, most obviously the volumetric cloud sim. The Animal Crossing team maybe could, but I don't know how big of an overall benefit they would get. Animal Crossing has a distinct look that I don't think requires a lot of the fancy features of UE4 and New Horizons seems to be doing quite alright anyway. Splatoon is another matter, but again I feel they get most of what they need from their current engine and rebuilding their proprietary mechanics in UE4 just wouldn't be worth it.
The two teams I could see benefitting would be the Fire Emblem team and Game Freak (who isn't internal but still). Neither has extensive experience in console development of high end, 3D games. Much less HD development. Now Sword and Shield and Three Houses don't look terrible, they're fine, but they are lagging noticeably behind the other big hitters. Now Pokemon I am positive is feasible in UE4. Fire Emblem should be, but their new emphasis on rendering lots of battalions could throw a wrench in that. But still worth investigating.
So tl;dr, for the most part no, but there are a couple of exceptions.