Okay, first the disclaimer, I'm NOT an electrical engineer but I've got a reasonable number of years on doing wiring on aluminum and steel boats. So here is my understanding in layman's terms.
Most marine engines do not use an insulated ground return circuit(where the alternator is electrically isolated from the motor and then connected to the battery via a cabled return), but they also don't use a ground return circuit as per in a car (where the alternator is wired to the engine block and the chassy/hull acts as the return path to the battery). Marine engines usually use a hybrid where the alternator is not electrically isolated from the rest of the motor BUT IS wired directly to the battery with a heavy gauge cable providing a path of least resistance from the alternator to the battery. In this system you are not going to get much/any flow from the alternator/engine to the battery as the cable between the alternator and the battery provides much less resistance than any alternative path and electrons always follow the path of least resistance. Your motor still has a ground strap to the boat to ensure that that there is never an electrical voltage variance between the motor and the hull, which could result in a lethal shock, but this ground connection is not being used by the alternator as an electrical path to the battery due to the heavy gauge cable connecting the alternator directly to the battery.
I know zero about black boxes but I'm going to assume that the ground to the hull from the black box is playing a similar role in ensuring that your downrigger wire and the boat are electrically neutral to each other, ensuring you are not going to get zapped. If I ever installed a black box on a metal boat I'd be doing a lot more reading about them and I'd ensure I had a way to isolate the circuit from the boat when I wasn't actually using the black box.
Moving on to electrical appliances like downriggers, radios etc. On a boat you want to provide a cabled path of least resistance between the negative, appliance and positive as opposed to having your hull as part or all of the circuit. If you use your hull as the circuit then any less noble metals attached to the hull are going to act as a sacrificial anode and you are going to have corrosion happening. The best case scenario is that you only start going thru your zincs quickly. The worst case scenario is you start loosing thru hulls or the hull of your boat itself. Unlike with your motor where we are using heavy gauge wire for short runs from the alternator to the battery, most of our electrical appliances have longer run light gauge wire connections. This means if we accidentally provide a connection from the battery to the hull, and from the appliance to the hull, the hull has the potential to be the path of electrical least resistance and become part of the circuit leading to the flow of electrons to the least noble metal along the way which means corrosion.
All of the above info relates only to DC circuits and has nothing to due with the issues of electrolysis caused by incorrect grounding/ neutral handling when connecting to shore power. Separate topic all together.
I hope this simplified (?) explanation helps, but would not be surprised if I only ended up confusing lot's of folks, but hey you didn't have to pay me $80/hr to confuse you like you normally would at your marine shop
When we did a bare bones rebuild of a 40' metal tug boat one book we found invaluable was "The Boat Owners Mechanical and Electrical Manual" by Nigel Calder I'd recommend it as a good overall reference manual if you are going to get into the guts of your boats systems.
Chow,
Ian