In all honesty, there probably wouldn't be any meaningful change in boat/ship development resulting from scientific evidence confirming the existence of modern megalodons. If they are proven to exist, then that means we've been coexisting with them for the entirety of human existence on Earth without any noticeable interaction.
Humans (and boats/ships) simply aren't a natural prey item for megalodon (any shark, to be honest). I would expect encounters to be more along the lines of current human-shark interactions: the shark investigates, the human panics, and the two go their separate ways. Sharks aren't malicious and have no ill will towards humans; I see no reason megalodon would become hostile once we've proven it exists.
In short: There wouldn't be a change in design with definitive proof of a modern megalodon.
Instead, there would be a massive push for research into common hunting grounds and migration paths to reduce the chances of an encounter.