Separate binary files have individual hashes, which are included in the package manifest file. The manifest is then signed, so a single signature covers all hashed files in the manifest.
Curiously though, in all of the MAS apps I've checked, bundled dylibs are explicitly not hashed in the manifest. This is the developers choice, but perhaps a default?
No. That's not how it works on Mac OS X today, where bundled shared libraries are supported.