According to the ArcGIS Enerprise documentation (Prepare data to publish a feature service—ArcGIS Server | Documentation for ArcGIS Enterprise) it is not currently supported to use ArcGIS Pro to publish a query layers that contains virtual columns, where clauses, or joins.
Query layers provide lots of flexibility to how we structure our databases and can help reduce the need for maintaining duplicate data. For example, there is an address point layer with address related attributes but we also have a table with information about waste collection that references address ids. If publishing the query layer with a join were possible then we could use a query layer to join the waste collection attributes onto the address point geometry, and display that in ArcGIS Enterprise. Without this feature we need to resort to using another tool to sync maintain a new layer that contains address point geometry and the waste collection attributes.
Providing the ability to publish query layers with where statements and joins gives the user much more flexibility in how they can manage and serve their data.