Mathias,
Looks like you provided a lot of valuable information here but I must still be missing something. I went to my web maps json and found the "id" of the layer I want to hide from the Layer List widget.
Then I followed the previous instructions and went into the widgets folder of my application, went to the Layer List widget and updated the config.json with the "hide" info.
Then I continued to follow the instructions and went to the LayerListView.js of the widget and made what I thought were the appropriate adjustments.
But so far it's not working. I can still see TransportationLabels at the top of my Layer List in my application.
I'm not sure what I'm missing. Any info or recommendations from anyone would be greatly appreciated. Just for reference I am using the WAB Developer Edition version 2.0. I created the web map in ArcGIS Online (hid the layer from the legend in the web map in AGOL). Used that web map in the Developer Edition builder, downloaded the app, added it to my server. It is currently available (gis.gillettewy.gov/DiscoverGilletteWAB) but I'd like to remove that layer from the Layer List. It was super easy to do in Flex so far not so straight forward here. Any thoughts?