Yes, but the infection is confined to the ship. And no, the clock is not "reset" every time an infection shows up. By now, just due to the factors you cite, everyone on the ship has been exposed. But even so, so what. See first line..."the infection is confined to the ship".
On old-time sailing vessels on long voyages, there was always a surge of illnesses on leaving port, but once that passed, the surviving crew was very healthy, as they had proven to be immune.
On Cruise Ship Quarantined In Japan, Any New Cases Would Reset The Isolation Clock
NPR ^ | 02/07/2020 | BILL CHAPPELL
Posted on 2/7/2020, 4:46:31 PM by SpeedyInTexas
http://freerepublic.com/focus/f-news/3814573/posts
As to your second point, the infection is confined to the ship, not really as it is worldwide now. But just as we would pull Americans in an Embassy out of harms way I guess dont understand why this is not the same thing. If they are there long enough, they will get infected.