I have a MapService published to ArcGIS Server 10.6.1. The data comes from a local FGDB.
In the MXD when authoring the document to define the service I set the aliases:
Because aliases in the FC in FGDB are not good:
Field properties set in ArcMap are exposed through the feature service; this includes field aliases
But I could not find any information about this in MapSerivces.
I tested this in my ArcGIS Server v10.7.1. It definitely works there. I changed alias for couple of fields in MXD and then published the service. When I query or click on the layer for pop-up etc, it shows alias from MXD and not from FGDB.
Check the REST endpoint for that layer and confirm the alias is correct as per MXD. Example below: