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PHP ships with prehistoric libzip 1.1.2, which doesn't support the encryption and few other things.
The documentation nicely states that this requires at least libzip 1.2
New release should ship with at least the version of library they recommend in the docs. But preferably it should ship with the latest available which at the time of writing this bug report is 1.3.2
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the zip extension rely (by default) on system libzip (all version >= 0.11 are supported).
The bundled version is indeed outdated and SHOULD not be used (the --without-libzip option is there only for some travis issues)
As for all libraries (openssl, libicu, libsodium, etc) using a bundled library doesn't make sense, and thus bundled library MUST be an exception (e.g. timelib)
So, not a bug.