I can see this behavior in 10.3.1 as well, however, it looks like the behavior is fixed in 10.4. There are a lot of fixes made at this release (10.4) for querying the available objects and general performance.
Are you able to test or work with 10.4?
I don't have access to 10.4 right at this time, but I'm going to want to deploy an ArcGIS Server 10.3.1map service with these materialized views. So even if I had 10.4 desktop, would it even work with ArcGIS Server 10.3.1?
Not with PostGREsql but this is the same with Oracle I believe. Are you trying to use query layers to access the Materialized View with spatial data? Without spatial data? With Oracle, to oversimplify, Materialized views don't support geometry.
Postgres materialized views work in ArcMap 10.5. Not sure about 10.6. The geometry column needs to be named shape and you need a unique identifier column in order for all of the rows to show up.