Figured it out myself.
If anyone else comes across this and wonder, Ii was a style/css issue, even though I added some styles for the legend in the css I hadn't looked through the (very long) style.ccs-file for LayerList. It already had a part with legend-styles where some parts (the missing ones) had the display property set to none which explains why they didn't show up.
/*********legend css from LegendDijit************/
.jimu-widget-layerList .esriLegendService {
padding-bottom: 0;
}
.jimu-widget-layerList .esriLegendLayerLabel {
padding-top: 0;
height: 0;
display: none;
}
.jimu-widget-layerList .esriLegendServiceLabel {
display: none;
}
.jimu-widget-layerList .esriLegendLayer{
font-size: 12px;
}
.jimu-widget-layerList .esriLegendMsg{
display: none;
}