Ah, so since 9-11 involved planes, let's drop all our other security and just focus on airports. Brilliant!
There are two things we should be concerned about, in my opinion: dangerous individuals and small but deadly packages.
Both are extremely unlikely to arrive via shipping container while they can still arrive by plane or truck.
A 20 year old terrorist of Jordanian extraction with a Spanish passport and no criminal record coming on a work visa is far more likely to arrive on a plane than to be packed into a shipping conmtainer for weeks with a carefully concealed water and food supply and air-conditioning source, the connivance of a number of crewmen, the bribing or deceiving of multiple harbormasters, forging of inventories, etc. at the enormous personal and financial risk of dozens of individuals and multiple corporations.
A small and dangerous package is less likely to enter the US via a port, with police and inspectors and receiving managers and dogs and metal/radiation detectors than it is to arrive in the dead of night over the Canadian or Mexican border in the trunk of a used Honda.
Terrorists, like anyone else, are risk averse and avoid overly complicated scenarios with numerous risky steps.