Put component designators on the PCB's silkscreen in KiCad
KiCad treats the designators differently than the normal silkscreen (not sure why), but as long as they are visible (right click, select "visible" - it looks like yours are set to "invisible") then they will be on the final gerber.
Any text set to invisible can be set not to show by selecting the "render" tab (top right) and deselecting "hidden text".

See the greyed out designator in the below clip compared to the others for an example of the difference:



You can confirm this by plotting the top silk layer and checking in GerbView. Notice that the greyed out designator C8 isn't plotted on the gerber.



P.S - The KiCad-users mailing list is an excellent place for enquiries, features suggestions, bug reports, etc.