So how come he didn't get court martialed over all those shuttles?
He knew who took them (Chakotay) and who crashed them (Chakotay).
Paperwork is about knowing where something is, or the burning wreck of it.
And every time after Chakotay crashed a shuttle and did not return it to Kim, then Kim made the XO fill out an accident report and shifted all liability from his lap.
You see, what should have gotten Kim in Trouble is how Seska snuck a fricking replicator off the ship and he didn't notice.
That's the same as you coming home from work tomorrow with a photocopier.
How shit is your office manager if s/he doesn't notice till after the new year?