I don't think you really need to worry about this very much but it is interesting that you are looking into it. Most folks probably never even give these 2 ducts a second thought. I know that I don't. But I am getting more curious based on your observations. These are my thoughts ...
You have 2 cowls on your stern. One duct is probably for passive ventilation and the other for the blower. It doesn't really matter that they come into the compartment low and together. They don't really have to function whatsoever. Some boats don't put any duct ventilation in at all. I had a boat with a diesel engine that had no ducts or blowers, just a lot of empty space under the cockpit that provided all the air and ventilation necessary. Diesel fumes, while annoying, are not volatile like gasoline fumes. I ran my engine for a 1.5 seasons before even noticing that I had a blower switch (it is down around shin level). Every once in a while I turn it on, but I find the blower loud and annoying. Passive ventilation seems to be enough because I rarely run the blower when motoring (I usually turn it off before very long) and I don't find any objectionable smells in the berth down below. I'm fairly sensitive to objectionable odors.
To be sure, it's good practice to run your blower when motoring. It does a good job for ventilation and helps to keep the motor cool, I suppose, but I've never noticed any difference. The other duct is probably passive and provided just for redundancy, I suppose. Sure, the fact that they enter the engine compartment in the same location is a little stupid maybe, but it doesn't matter and there is limited space under the berth, so who is going to bother trying to make another passage? When the boat is moving forward (either motoring or sailing), there is slightly negative air pressure surrounding those cowls and the passive duct is still drawing air out of the engine compartment. A better design for passive ventilation would be to have a cowl facing forward where the air pressure is positive and a duct coming into a high area in the engine compartment. That would work similar to the way attic ventilation is designed where air comes in at a ridge vent and leaves through a soffit vent. I'll bet some high-end boats have this thought out, with a dorade and duct providing some positive air flow.
It's good that you are looking into it. By all means, if you have ripped or damaged ducts, it would be a good idea to replace them. As you may be able to tell from a lot of vague responses, not many people put a lot of thought into these features. They are pretty much out of sight, out of mind and don't often lead to troubles that cause people to dwell on the ventilation. If you are able to trace those ducts, I'd be interested to know your findings. You've stimulated my curiosity, so I think I'll pay attention the next time I'm crouched inside the rear lockers chasing cables!