The below discussion is related to engines that are mounted below the water line or can be below the water line when the boat is heeled. Thus many power boats don't have an anti-siphon. But most sail boats do have it or at least they should have it.
I think we might be confusing one another by "upstream" and "downstream". There is no vented loop in the hose that carries sea water between the through hull
and the raw water pump. The outlet of the raw water pump generally feeds water through one or more heat exchangers. It might cool the oil
of the engine and/or transmission
. Then the sea water usually goes to the main engine heat exchanger last. In this entire path from the through hull
to the engine heat exchanger there is almost never any vented loop or backflow preventer.
Once the hot sea water leaves the main engine heat exchanger the water hose usually rises up to the highest possible point in the boat. There it will pass through an anti-siphon device. This device will be open if air is present but as soon as water hits it then it closes. Some boats (like mine) don't have a valve but they have a small hose that goes to the hull and lets a little water dribble out. Then from this high point in the system the hose goes down to the exhaust elbow. This anti-siphon must always be above the water line at all angles of heel else the anti-siphon feature will not work. That is why it is always as high as possible above the engine.
As soon as the raw water pump stops running some water will still flow down from the high point into the exhaust manifold. This will create a small vacuum at the high point and air will enter the hose there through the anti-siphon. This air stops any chance of siphoning action. If this high point does not allow air to enter because the anti-siphon device is plugged up with gunk then water can continue to siphon from the ocean into the muffler. Eventually the muffler will fill up and then the siphon will continue to fill whatever cylinders of the engine happen to have their valves open.
Some boats have a high loop in the exhaust hose. This is not what I am talking about in the above discussion. The high loop in the exhaust hose is just there to prevent water from being pushed into the muffler from a following sea. It does not usually have any anti-siphon device. There is too much risk that exhaust gases might leak out into the interior
of the vessel.