You are right, a "solution of NaOH" contains Na+ and OH- ions, not NaOH molecules, and a "solution of HCl" contains H+ and Cl- ions, not HCl molecules. But it's simpler to say and write "a solution of NaOH" than "a solution of Na+ and OH- ions". So we do. After all, it's what you get when you dissolve NaOH in water, so it's justifiable to call it a NaOH solution, as long as you are aware of what that is chemically.
The reaction that takes place is not between NaOH and HCl molecules, but between H+ and OH- ions. Na+ and Cl- are called "spectator ions"; they are present but don't take part in the reaction.