As I understood it, Khan originally hid his people in the torpedoes with the intention of sneaking them away from Marcus, but then something went tits up between him and Marcus and he thought Marcus had killed them. After Marcus got wise to Khan's plan he stuck all of the torpedoes on the Enterprise with orders to fire them at the Klingons- cleaning up his own mess and starting a war with the Klingons at the same time.
Those things must've had a helluva range originally, as Marcus expected them to still hit Kronos with the human popsicles inside. But as Khan indicated that he at least had a hand in designing the torpedoes, he may have allowed for the the necessary space from the get-go. It doesn't seem like a particularly safe way of smuggling people covertly, but the torpedoes have their own engines, guidance systems and stealth capabilities... so why not? Especially with Marcus looking over his shoulder. A transport ship designed for 72 large crates would likely have drawn suspicion.
I'd imagine that all 72 torpedoes would have suffered surprising guidance system errors and vanished without detonating if Khan had been able to bring his plan to fruition.