Just watch it if you have limited edition sets
Speaking as someone who has done it myself, the process is extremely painless. The form is as non-invasive as possible, as you just need to fill out your personal information and shipping details, and you’re good to go. From there you’ll get a free label for up to four Joy-Con: if you want to do more, you’ll need to fill out another form. The “reason for repair” line is even optional, so that’s what I mean by “non-invasive.”
So there’s one big catch that you really need to be aware of before you do it, and Nintendo does note this on the site (albeit coldly): if you’re sending in colors beyond the standard gray, neon blue, or neon red, there’s no guarantee that Nintendo will send the exact ones you gave them back. You need to check a box to agree to that, but I’m sure some people might miss it, and it’s kind of important given the collector value of some of these controllers.
As a bit of advice, I recommend just doing this process now if even one of your backup Switch Joy-Con is drifting: even if it’s a pair you don’t use anymore, or if it’s just one of the two in the pair that’s doing it. It’s free, so you may as well take Nintendo up on it while the going is good, before your main pair bites the dust and you’re left with two pairs of drifting Joy-Con.