Innocent until the courts say otherwise. It's why we apprehend people for crimes instead of just shooting them (in most countries)

Likely, a narco-sub, but still should intercept and board rather than summary execution.

i have not seen any submarines with flags though.

I think GP means flag as in flag state - ocean vessels are typically to some country. In this sense, nearly all submarines are flagged - US navy, Russian navy, whatever.

Not as in a literal flag flying on the submarine. (Though they do fly flags near ports and such)

Their is an entire DIY submarine community around the Caribbean and those guys aren't part of any navy or military and don't fly flags.