You'd still get your check and your overview.
What I had once, was I was in a rush to get the time bonus, and then I docked, and then I clicked through the missions that I had, cashing in each one, and each one taking 10 seconds to connect, load, bring up the silly reward screen. And by the time I was halfway done with the missions, my time ran out.
Just cash them in all automatically. Heck, if you want you can even force open a multipage report, clicking through each mission report individually and close them all at once. Just don't make me click 50 buttons for some info I don't want. (20 missions, each time taking 5 seconds to load, 20x back in the report screen + selecting mission board, factions, and various other overhead)
I don't see the point in waiting for mission payouts after docking.
The only thing I can possibly concieve is that you want to come out of dock again and have that pirate intercept you, so you can get your 10k credits for the kill or something like that. Nobody would do that kind of thing. I'm happy if I can cash in my missions quickly, and not be interdicted 3 times in the last light second from the station...
But that might just be me. If there is a problem with auto cash missions, then have it an option, or ask the player when they open the mission board: "Do you want to cash in all missions here?" or have a checkbox system, like they do with the ship rebuy screen.