If you're speaking of the Ehime Maru, it was a school ship, not a research ship. But close enough. When we look at the damage to Ehime Maru, we see some things that immediately distinguish it from the damage to Estonia. First, the damage is below the waterline, because that's were submarines operate. Second, the impact damage is spread over a wide area, consistent with impact with a blunt object like a submarine. Third -- and most telling -- there is a giant skid mark from USS Greeneville's anechoic material.
The damage to Estonia is above the waterline, not "at" it. It is highly localized. And there is no transfer of material from the impacting object. And no, those elastomers don't just magically dissolve in seawater, as you claimed.
There's still the matter of the physical effect you haven't considered in collisions, which undermines that claim. I've asked you to describe it and its effect, and I've asked you in a way that you can't just Google for the answer. You have to answer from a position of prior knowledge. Can you do it?
The technology that enables it enables it for submerged operation only, because the fluid dynamics for a submerged submarine are wholly different than those for a submarine on the surface. Sensibly enough, the designers optimize for submerged operations because that's where a sub is meant to be.