the risk is indirect. its not like the Emir is going to walk into a DPW board meeting and say "when do we ship the nerve gas to NY". the risk is that the company management is infiltrated by what appears to be "normal" people from the UAE, perhaps they hire some stateside subcontractor to work at the port that hires "clean" jihadi symapthizers (let's face it, we have plenty of them inside the US already). in addition, this state owned company will have easier mechanisms for visas to the US, given they have a business presence in 6 major cities. now you have a conduit through which some operation can be planned and carried out.
there are plenty of legitimate security concerns, and improvements that can be made. if the administration would start proposing some of them, they might be able to get themselves out of this political mess - save the deal - and maintain this "UAE is a great ally" relationship.
There are risks everywhere. UAE is not going to risk having us as an enemy.
In every port they have operations, the local natives are in charge.
If you haven't read this, you should:
Article in upper left hand corner:
Ports & Politics - the UAE/P&O Deal
http://www.globalpiracy.com/