Japan used explosive motorboats during World War 2, building thousands. They were not as effective as planes, I'd guess due to difficulties in evading defensive fire.

https://en.wikipedia.org/wiki/Shinyo_(suicide_motorboat)

I'd imagine a larger boat would be even easier to sink.

If you do not need the internal volume you could fill it with something which even with hole would still float. I think you could find some reasonably buoyant material that could take some beating. And on other side I think there might have been changes in ship construction and armaments which might still make this approach valid for a while.