We're working to add that functionality to narrow down to one copy across the multisite install, but it's currently on hold for other work. Our goal is to have that launched by the end of the year -- December 2019.
Media Deduper can be network activated. It won't be confused by the presence of other sites on the network, but that's because it will simply see each site on the network as a completely separate instance of WordPress. Because of that, MDD Pro may also ask you to enter the license key separately on each site and there is no network-wide admin screen.
If one site in the multisite install has multiple copies of an image, MDD Pro will help you get rid of the duplicates. If each site in the multisite install has its own copy of an image, MDD Pro will NOT do anything to help you narrow that down to one copy across the entire multisite install (yet!).