There is one truism that has been constant throughout my career on the web, and it’s this: naming things is hard.
Trent talks about the strategies out there for naming things. He makes specific mention of Atomic Design, which as Brad is always at pains to point out, is just one way of naming things: atoms, molecules, organisms, etc.
In some situations, having that pre-made vocabulary is perfect. In other situations, I’ve seen it cause all sorts of problems. It all depends on the project and the people.
Personally, I like the vocabulary to emerge from the domain knowledge of the people on the project. Building a newspaper website? Use journalism-related terms. Making a website about bicycles? Use bike-related terms.
Most importantly, make the naming process a collaborative exercise, as outlined by Alla and Charlotte.