Some missions grant bonus points, such as objective markers to be claimed or succesfull rear shots. At the end these points are added to the killpoints. This still applies is one of the players has lost all his ships.
Some other missions grand additional points by doubling the point cost for an objective ship. However, if all ships are destroyed, the fleet is worth 400 points. Do you still get the additional points of the objective ship? The obective is worth double the value, but your whole fleet is worth 400 at the end, regardless of the value of the individual elements.