"Could care less" is the opposite of false double negatives, like "I don't care about nothing," where nobody constructs the meaning directly out of the syntax, but English speakers try to shy away from them or they seem uneducated.
"Less" seems like a negative, so pairing it with "couldn't" seems like a double negative, so they switch it to a single negative. Out of habit, they don't construct the meaning out of the syntax; the meaning is contained in the phrase "care less," a vague emotional conveyance of their low level of caring.
People use language differently, and this expression is common enough that it will never end. What could be ended however is the rubes who pointlessly say "have a nice rest of your day."