Foam, I don't think, would cause those distortions. Clearly, if you bought the boat new that way, the dimples were "built-in" and not a result of any repair work. Also, the condition is symmetric which leads me to think that in assembly some component, possibly the stringer grid, was jamb-fit somehow and not trimmed to fit as it should have been. I doubt the condition is any more than cosmetic. Maybe the guy who restores it in twenty years or so will pull the deck off and discover the cause.
If you can, post a picture or two of the dimpled areas. Maybe someone here has the same hull condition and will offer some other thoughts.