I can't think of a reason why we wouldn't board and check them out if we knew they were out there, so I tend to think that we wanted someone to know we have an eye on shipping, or that we want someone to assume their ships are still out there and not captured or boarded, or that the lawyers haven't sorted through the international legalities yet and we're holding off for them, or that we're in the middle of an investigation and need to build a case by gathering as much info as possible for the state department's legal team, or some other thing.
I do accept the fact that al Qaeda, Iraq, Iran, Arafat and others have at different times used ships to smuggle assorted materials and arms, as we or other nations have caught them in the act. So I discard the sensational parts.
Sometimes I think reporters include "impending crisis of gargantuan proportions" because they have other than honest intentions.