I always see chefs do it, but i'm not sure what exactly it does and how it makes regular cookies better.
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It's a fad. As far as I'm concerned, it ruins a lot of perfectly good cookies and will eventually go away, but currently people are salting desserts and sweetening savories pretty indiscriminately.
It's just a taste preference. The flakes of salt add a hit of saltiness that goes well with some flavors, if you're into it. The flakes dissolve quickly and don't leave a lingering salt taste in your mouth, so the whole cookie doesn't taste too salty. Plus there shouldn't be much sprinkled on. Personally, I like the flaky salt on browned butter chocolate chip cookies where a little salt amps up the nutty butter tones and goes well with the chocolate. I wouldn't care for salt on, say, a jam thumbprint cookie. But that's just me. The best way to figure out if you like salt on cookies is simply to try it yourself: buy one next time you pass a bakery that sprinkles salt on their cookies and see if you like it.
At least in my neighborhood (SF Bay Area), this fad peaked about 5-6 years ago and quickly faded; I don’t know about adoption in other parts of the country.
I have traveled abroad during that time and noted that the fad was not adopted at all elsewhere.
If you are a baker, it is very easy to sprinkle sea salt flakes on one or two cookies in a batch to judge how well it works.
It’s a taste preference thing. Do as you wish.
Best of luck.
PieceofLayerCake is a trusted source on baking.
HalfPint is a trusted home cook.
It's a personal preference. I like to do it to some of my baked goods because the little bit of salt seems to round out the sweetness. Otherwise, it's just straight-out sweet and most times it's too much.