Game manual states that Alex was going to be picked up by 'a comfortable ship' (seems like not the North Wind), but he 'accidentally' encountered North Wind which was drifting in the ice all these years and obviously was not found (or just nobody bothered about it - nothing valuable on board and it's difficult, if not impossible, to reach it).
Men in arctic suits - you mean dead sailors? Or someone else?
Alex actually helps Kronos in the strange fight near the end of game, so it seems that the timeline where North Wind became a nightmare was for some reason wrong (well, it's wrong for sure
) and Kronos tried to set things the way they should be. In the end, player actually chooses how he would correct this (by going along one of the Kronus fingers).