And a lot of writers use them, too. And they help add color to the world. Even if you have sensibly enough given all your characters distinctive names, they might still have bynames to lend color. Sure, you don't want to ladle twenty Johns on your hapless reader, but John Mortimer's son at least hints that there are other of that names.
But they tend to overlook how people acquire them: by having something distinctive about them so they can be told apart. But what is distinctive varies from person to person, and so will bynames. There will not be a system of bynames.
Well, usually. I've seen Name of Place occasionally. That only works if this is the only person (of that name) from that place. Works for nobles if the places are small enough to have only one noble per -- though that's pushing toward a title. And patronomics are common and realistic, but John Johnson has its limits as a distinctive trait.
Name the Adjective -- at the very least, some of them are probably going to be called Adjective Name. "Little John" "Black Bart" -- etc. And in chosing the adjective, they tend to favor character traits too much. Physical traits tend to be more common. "The Fat" or "The Pale" -- which leads in the other issue, which is that they tend to be too flattering. To be sure, we are hypersensitive to offense. One American sociologist told a Chinese man known as "The Stutterer" that it would be considered rude in America, and he was flabberghasted. He stuttered. How on earth could it be insulting to point him out by such a distinctive trait? But even if you, with an eye to your audience, avoid such names, there are still a lot of neutral ones to pick from.
And I really, really, really hate the compound noun byname where the nouns weres just stuck together. "Moonleat" say, or "Eaglestorm". Bynames tend to have transparent meanings, since they are generated by people on the spot to refer to obvious traits.