Same here with missing popups. In our case we have two layers with a disjunct definition query. One layer shows features with a specific attribute set to 1 (e.g. A=1). The other layer shows all other features (A<>1). One of this layers renders the popup, the other not.
A query directly to the REST endpoint shows, that the service and the layer are ok. The correct data is queried.
It's definitely a version problem in the Maps SDK. All popups are ok with version 4.24 and 4.25. Starting with version 4.26 up to 4.30, one of the layer doesn't render the popup. The build-in Map Viewer in the portal shows the popup, because it's running with 4.24.
So far we don't know what to do. What circumstances cause the popup not to render for an arbitrary layer? Any suggestions Esri?