Haddock's prune option is not regarded for DEPRECATED things
I introduced this regression when I extended Haddock, so that it adds deprecation messages for deprecated things to the generated documentation.
This may not sound critical, but it is a rather common use case to prune documentation for deprecated things. That way you can keep deprecated stuff around for backward compatibility without cluttering the documentation.
I'd tend to disable the feature for now (a patch set is on my disable-support-for-warnings branch).
Alternatively we could apply a fix for the issue. I have a patch set for that on my fix-warning-support branch. But it is not a trivial change.