One, does this happen even if the sub rams while surfaced?
No.
And two, does the immediate S move action interrupt a captain action?
Therefore, no. The sub can’t shoot while submerged, and has no S segment to move while ramming on the surface. The S segment is not a move action. The Nautilus would actually shoot at the Bon Marin before applying ram damage in that example if she was on the surface, because the order of operations goes move>shoot>ram>board.