Any program like 7-zip that has a command line version can do what you want.

The main thing is to be sure that all the zips you unpack really do have everything organised correctly and don't have files with the same name (variations on ReadMe and License or the usual problems) and while there are options to autorename rather than overwrite, you're still left with no way to connect the duplicates with the corresponding content.
Even if they do, it would still be better to unpack into a temporary directory rather than straight into the main Runtime..