The most common and most likely answer to this crossword clue is the 9 letter word DEADLIGHT
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More clues leading to the result DEADLIGHT
Buddy explains!

The straight part
We know that "protective cover for ship" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case protective cover for ship = deadlight.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does DEADLIGHT mean?
DEADLIGHT noun- A strong (often wooden) shutter fitted over a porthole, that can be closed in bad weather to keep water out and discourage the glass windows from breaking.
- A deck prism, a device to allow light into the cabin of boat through the deck.
- An eyelid.