They aren’t always helpful. For example, note that the “Wilderness Explorer Logo” badge has a pink dot by it:
However, when I tap on that badge, the store tells me I can craft “Lots” of it, meaning over 100:
So I dig a bit deeper and craft some of the sub-badges for the offered badge:
And what do you know, all of a sudden the store realizes I don’t actually need that badge after all:
And there are times when you don’t strictly need a badge at the time you go to the shop, but it’s one that you run out of all the time and so is worth buying anyway. For example, the shop doesn’t have “Buster” or “Platinum You Can Fly” marked, but I have only one or two of each of those and frequently need to farm them, so it’s worth getting them even though they aren’t marked.
Going by the pink dots is better than just ignoring the shop or just buying as much as possible every day, but it’s definitely not the best use of your badge tokens.