This is the reason the US and USSR worked so hard to kill cheap commercial space flight in the 1980's.
About scientific projects I doubt it will ever happen because you can simply find a group of American researchers to collaborate who probably would be open if the research advance their field, about companies I'm less sure, they can simply put extra regulations because of idiotic nationalism, for example do not allow a German company to use a Falcon rocket because it has sold some type of cheap telecommunications equipment to Cuba for example.
I think no one that is sane will enjoy SpaceX doing clearance sales of old rockets to warlords in Somalia.
EDIT: As I understand SpaceX do not intend to sell rockets but just the service of having rockets and selling launches. But I can be wrong about that.
Maybe they look for a reentry shield and radioactive emissions or something, but I don't think it is much of a risk since the blowback from trying to sneak a weapon into space would immense, the risk of discovery is high (satellites weight much less than nukes or kinetic weapons) and you will have just given the world community all the evidence it needs to prove you did it (nuclear weapons and satelite payloads are very traceable).
Of course someone could get a satellite launched that maybe has enough fuel to change orbits slightly and could be used as a weapon against the space station or other orbital assets. The difference between a satellite and an orbital missile is software and maybe a small delta in fuel.