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.