If you use the floating islands world type and set it to beach, it causes shipwrecks to generate partially in the void, causing them to get cut off. As a result the sometimes do not have chests.
Example
-9208981173496188401 @ 90, 0, -720
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We're tracking this issue in MC-128659, so this ticket is being resolved and linked as a duplicate.
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Brevort
Duplicates MC-128659