Or just leave some credits, then we will be able to buy another vault and have more room for more items.
Genereally don't deposit random junk, try to leave uncommon or rare items, because all the other stuff is fairly easy to come by. That way the fleet bank remains interesting and might not be full ALL the time.
Sometime in the near future I would love it if the items in there continually evolve to rare or very rare.
Also if you get a new ship for example don't and and buy stuff expensively, look into the fleet bank first to find what you need.
That's what it's there for, it's a resource pool for all the members.