Does playing the harp ever become second nature?

Everyone is different in how they internalize experiences.

I'm always thinking about what I'm doing. But foremost in my mind is the series of musical phrases I'm creating, and the impression Im trying to create in the listener. Then comes all the details - what impression a note will magainst a chord, where that note is on the harmonica, and finally the set of concrete actions will produce that series of sounds on the harmonica.

But that's me.

You may not carry all that stuff in the forefront of your awareness. Or maybe you do and feel burdened by it. If that's the case, then internalizing that knowledge to the point where you can call it up without having to think about it may help.

Some folks seem to just play without hearing the result what they play against the chords or the rhythm, often just reciting stock licks. That's not a desirable practice or result.

Listen to the Walters or Sonny Boy II. They always knew exactly what they were doing and did everything consciously and deliberately, to great effect. Did they think about music theory? Probably not, although they always played the right notes. Did they think about hole numbers and what their tongues were doing? Impossible to know.

If you're just talking about whether you have to think aout hole numbers, breathing in or out, and bending, then I think that as you gain familiarity with them, you need to think about them less and less.

When you first learned to drive a car, you probably had to think about every little thing. Later, you find that you go through a complex series of actions without thinking about them - swerve to avoid that car that pulled out without warning - how did you do that? Slow down when the cars ahead do - how did you do that? You can describe how you did it, but in the moment you didn't think about how, just the what. Everntually you'll approach the harp the same way.