Hello Commanders!
We're not against the concept of reducing payouts for crew not currently onboard your vessel. An argument could be made that even though they are still on retainer, they don't get "danger money" payment when on shore leave.
We'll take this under consideration (no ETA, no guarantee) for a future update.
% of all earnings when active. Flat fee for inactive. There's no reason I would ever give an inactive crew member a percentage of a trade run or mission I did without them.