A sub could be a rewarding and fun hobby but will not be simple or cheap to build.
Being bombed as a terrorist threat is not a concern.
I doubt whether you would build one that runs in the ocean and could go deep or fast enough to be taken as hostile.
For personal use as far as I know you only need to register it as a boat.
Also, for your personal safety, being a certified diver would give you a lot of the info you need about being underwater.
I havn't had a chance to see it but a fellow near here has built one that is shaped like a sub with a coning tower and working periscope but doesn't submerge.
A submersiible would take a monumental amount of dedication to pull off.
Here is a link to a site where you can get more info on this.