This effect can be diminished or even done away with if your characters notice it themselves. But even there, things can get ugly if you don't justify the name, somehow.
Some names, of course, wear their meaning on their sleeves. Rose, Angelo, Honor, Maximus, Scarlett, Leo. . . and if they happen to be typical and plausible names for the era you are creating, you still have to have characters make lame jokes about a lion-tamer named Leo, but once you do that, you can run with it. (If the name is somewhat obscure, you can have a character whoop it up, and then explain what in the world is so funny about a sculptor named Peter.
Odd-ball names on the other hand -- perhaps you want to name your heroine Alyssum in Victorian England.
That's not a Victorian name.
Really, it isn't, and failure to grasp that there were rules and customs about naming is a nasty flaw in world-building. Parents who aim at the unique name for their child are commonplace in very few societies. A Victorian heroine named Alyssum had strange parents, ones who set out to give their daughter a strange and peculiar name in an era when it wasn't a strange and peculiar name like everyone else's.
Or perhaps she was named Alice after an aunt and is called Alyssum to tell them apart. The flipside of rules and customs about names is that you do tend to end up with dups.
But nicknames like Alyssum and bynames have even more scope for accuracy and Meaning, since they are meant to have meaning, even if they don't capitalize it. The odder the name, the more need to explain it at least. Robin McKinley didn't open Beauty with the lengthy description of how our heroine came to be named Beauty for no reason.
And naming someone is a characterization trait, since it tells what you think about someone else or yourself. The flamboyant social butterfly might opt for the last name of "Desiree Butterfly", but her retiring and mousy sister would probably aim for "Jane Smith" to avoid attention rather than "Jane Mouse." And the con man will not call himself "Joe Slick" but "Aidan Trueman" which is among the reasons that a solid, quiet, technical man would call himself "John Smith" rather than "Joe Reliable."
An Evil Overlord name like Ectar the Destroyer is the name of an adolescent wannabe. Perhaps he's grown out of it and never wanted to face the jeers for changing; perhaps someone ascribed it to him, and he did not want to stoop to such matters; perhaps he wants to pose as an adolescent wannabe. But there's got to be a reason for it.