I'm not sure that Timothy fails to understand the severity of their situation on the cay. Though Phillip knows that his father will never give up searching for him, Timothy recognizes that the little island is a remote one--virtually uncharted and in an area known as "Devil's Mouth" for its dangerous reefs. He knows that many ships will not be able to navigate the dangerous waters and that they may never be found. When Timothy decides that their failure to be rescued might be because of the "evil jumbi" there, he takes actions to rid the island of the bad omen. Timothy is also worried that their stay will be so long that he might not survive the ordeal, and this worry proves to come true when he dies protecting Phillip from the hurricane. The war presents another problem: German U-boats patrol the waters, making it unsafe for all Allied ships that may approach the area.
I'm not quite sure what you mean. Perhaps it was the problem with white smoke?