When I was constructed, the tunnel did have 3m of sediment on top of it. This was required, as the tunnel was dug horizontally. Unless that changed over time, no part of the tunnel should be exposed.
I do know that. But I think the graphics in Wikipedia visualizing the profile are wrong. I've been into exhibitions about it, which showed much more than that. Also it may have been different at different times because the river is dynamic, has been and is been dredged out, from time to time, as necessary.
The roof of the tunnel is too high in the water, to let contemporary large ships
pass. Where large ships means the giant container freighters with 19.000+ TEU capacity. Mission impossible. Covered or not. This is not true for roll on/roll off ferries, or some cruise ships which seem similarily large, but aren't, at least not below the waterline. They just manage, but barely.
It is a barrier inhibiting ships with large draft/draught from passing. Which is why all the terminals servicing them are downstream.
