We do have ScanSnap Home support being rolled out in Paperless 3, sometime in December of 2018. Until then, for Paperless 2, uninstalling ScanSnap Home  and re-installing ScanSnap Manager. SSM will still install on Mojave on the Mac on discontinued ScanSnap scanners without any problems other than the warning about future support for 32-bit apps, and it works just fine with Paperless 2.5.

Alternatively, until Version 3 is released, one could use ScanSnap Home to save to the desktop then drag and drop the pdf into Paperless. It's not the most elegant solution but should work for now.