You will get used to it, like I did. I mostly play handheld now. It's much more comfortable on my bed than the tv/couch
Takes a bit of adjusting. Analog sticks are more sensitive because of the short throw to the traditional controllers. Also definitely more awkward using the right stick for aerials, and I've noticed a bad habit of mine in avoiding using right stick aerials because of it.
What I do like with the joycons however are short hopping to aerials. The buttons are flat and closer together, and feels nicer sliding between the buttons than the GC and Pro controllers.
Durability of the joycons are questionable as my left stick got stuck upwards after a lot of hours mashing the crap out of it. Only bought my switch a few months before SSBU was released too. After replacing the overpriced joycons, I'm trying to preserve them by playing "slower" characters, like Ganon and Samus. I'm around 3.75 mil gsp ... respectable I think, considering its lack of ergonomics.
But yeah, I rarely get turned off from my technical limitations with the joycons now, although I reckon I'm gonna burn through many more left joycons and $$$ playing smash handheld.