All versions of WAD Manager are compatible with the 4.0 system menu. Installing correctly signed wads would work without problems(i think), but nobody can test it, because there aren't any correctly signed wads except the IOS. And the IOS are already installed.
What you want is being able to install trucha signed WADs, and that's possible in 4.0 with all WAD Manager versions too. You only need an IOS with trucha bug, like the cIOS.
PS: The unsoftmoaddable Wiis have a different issue, but even on them with 3.4 system menu the installation of IOS16 works without problems