I have the same problem: I am getting the result of my geoprocessing service with the correct symbology, but the labels are missing.
Same issue has been reported here: https://community.esri.com/thread/110710
Doss Dingli: Can you explain how you solved the problem? Thank you!
In my case the problem could be solved as follows:
The uploaded python script contained «MakeQueryLayer_management» (https://pro.arcgis.com/de/pro-app/tool-reference/data-management/make-query-layer.htm).
In order to display labels on the resulting mapservice, the "QueryLayer" had to be saved as a feature class first («FeatureClassToFeatureClass_conversion»; http://desktop.arcgis.com/de/arcmap/10.3/tools/conversion-toolbox/feature-class-to-feature-class.htm).