I believe there are four agents (the Captain, the Breaker, the Bathyphile and the Mondaine) and eight plots (Consignment without Contract, Found at Zee, Zailors Astray, Naval Intelligence, Beneath the Waters, Breaking and Entering, Infiltrating and A Disposable Network).
You can only have three plots of any kind running at once, so, no, you can’t have all your agents active at once. If a third type of agent is unlocked, then you would presumably be able to have one agent of each type active at once, which is a bit neater.