Do nails coming through the roof (missed the beams) need to be removed in order to maintain the integrity of the roof long term.

Missing the joist? A truss? Are these long nails? Short nails? Short ones would most likely be from reroofing. How old is the house? No need to remove but I would be more concerned about nails that should have hit the joist.

Of course roofing nails go though the plywood all the time