The documentation has a side note:
Unfortunately the Bitbucket UI will only extract issues where they are referenced by commit message, which is a shame as if you create the branch from the issue, you’d want all commits on that branch to relate to the issue.
It does explicitly refer to the Bitbucket UI, but in passing it could be taken to refer to the hook itself. Certainly customers are quite often surprised to learn that the hook does take branch names into consideration as well as commit messages. Perhaps the fact that this aside is the more prominent of the two mentions of branch names has something to do with it.