As a pilot that doesn't always have access to a mic, I use signals a lot. I often feel somewhat rude simply shouting orders at my crew when I don't have time to type something out.
My suggestion is to add a new helm signal for courtesy remarks. There's a spot for it right here:
This could a single command, which offers a audio / text "Thank you!" that a person at the helm can use to thank a crew member for performing a given action.
Or, it could be a menu that gives a few different friendly remarks including "Thank you!", "Good job, crew!", "Nice shot", "Give 'em hell!", or the like.
I see there is also a few gaps in the gun menu that could be similarly leveraged, but I think that's less important than the helm signals.