Is it possible to do a mass replacement of aging vehicles

This occurs because it takes time to load: proportional to the amount you are loading. When the first ship loads up, it leaves less for the second one to load, causing the second ship to spend less time in the dock, and therefore catch up to the first. As the second catches up, there continues to be less and less for it to load, causing an accelerating cycle that ends up in the state you have pictured.

The best way I have found to combat this is to make all (or all but one) of your vehicles wait until fully loaded. This causes less available cargo at the dock to mean more time at the dock. This reverses the cycle and causes your vehicles to remain relatively well spaced.

The a single vehicle on the route not fully loading will not cause this problem, as it will eventually catch and pass the fully loading vehicles ahead of it. Such a vehicle can be a good indicator of when you need to add or remove vehicles.

No, as near as I can tell resource coverage does not affect load/unload speed. Resources at a station naturally degenerate over time, so to get a higher% of hauled production, you need to have one vehicle loading at the station all the time. For part 2 of your question in one of my games, I had a station cover two coal mines with just 1 square on each, and I still transported 91% of the production.

However, one thing that does affect load/unload speed seems to be the station itself. If your train, for example, is longer than the track it seems like it takes longer to load/unload.

Also, all the cars on the train load simultaneously, so 10xoil tanker train will load more oil per 'tick' than a 5xoil train, but it takes approximately the same amount of time for both trains to reach 100% capacity (assuming enough oil at the station and it is long enough to accommodate both trains).