It's one of a million memes that all follow a similar pattern - you're meant to recognise the pattern and therefore that it's 'one of these memes'.
Very, very few of them are ever actually funny ;)
[somebodies] do it [somehow]
'do it' is always a double entendre:-
- do their job
- have sex
Carpenters do it with wood.
Window cleaners do it up a ladder.
Chess players do it on the table.
Farmers do it with sheep.
Nerds do it alone.
… ad nauseam.
Mushrooms grow in the dark, therefore mushroom hunters must hunt them… in the dark.
There may be actually an added implication [I don't know the movie so this is pure supposition]
People at the very bottom of any command ladder may consider themselves to be under-informed as to what is going on above them in the hierarchy.
There's another common meme, which may be salient.
"We're like mushrooms. Kept in the dark and fed on b***shit."