And yet Clerks does feature a few very fictional brands… because the characters discuss them and say some less than nice things about them. Nails, Chewly’s, Mooby’s, etc.

You won’t get in trouble for acknowledging the existence of McDonald’s.

But having a character talk about how they think the McRib is made of cat meat will most definitely get you sued.

There’s more to it than that of course, but as long as the filmmaker doesn’t seem to be actin in bad faith, wrongfully trying to confuse or mislead customers, or downright defaming the brand, it’s legal.

That said, it’s usually a lawsuit that establishes whether it’s legal or not, so to save money on legal fees and court costs, logos are frequently just flat out avoided when possible. Not for legal reasons, but to avoid the hassle of legal reasons.

Not a stupid question. But it is important to distinguish between copyright and trademark. Copyrights are the owner's automatic rights to the exclusive use of their artistic works, which in theory could include some logos, but most logos are probably too simple for copyright protection. Copyrights are non-permanent, but long-lasting, and they can't prevent people from using the work for Fair Use (which is complicated, but basically, think about whether the thing you're making with it could ever be a substitute; the movie Clerks is not a substitute for a product logo, so it's likely fair use).

Trademarks are registrations with the government to prevent other companies from using your company's identify marks. They are permanent, but can be lost if not defended—that's called genericide, and it's interesting, but irrelevant here. They don't protect all uses of a name or logo, but they do prevent someone else from creating a restaurant called McDonalds or a logo with the golden M.

What's important to note about both types of intellectual property is that neither prevents anyone from criticizing, covering, or making art about their owners. For example, a song owner can sue because you use too much of their song in your vlog's review, but it can't prevent from using a few short bars to talk about its unique time signature.

To bring it back to Clerks, the companies portrayed cannot prevent the movie from using their logos to make a point about their products, but they could prevent the movie from implying that they sponsored the creation of the movie.

TL;DR: you can probably include a logo in any artistic or critical work, so long as you don't imply endorsement or purposely sow confusion.

Coke probably won't sue you if there's a coke bottle in the background giving them free publicity. But if the scene is objectionable or if, say, you're using it as a prop instead of it being in its natural environment, then you might have issues.

Also, with music?

Can someone come at you for it?