The author of the quote certainly knew how to say "the ship was not seaworthy" and "the ship sank because it was not seaworthy". The author said no such things.

The author said:

He knew that she was old, and not over-well built at the first; that she had seen many seas and climes, and often had needed repairs...

and more, which you have already read. This is clear enough to me.

Suppressing your own doubts is not actus reus -- you need an action in physical reality.

In this case, an inaction.

And, legally, there is a LOT of difference between an act and an omission, failing to act.

In general there is, but not when the person has a duty to perform an action, knows it is required, knows the consequences of not doing it, and does not. That is the situation presented.