One...you don't just pull up to a containership in midocean...these things are tracked pretty religiously by lots of relevent authorities.
Even so, container seal inspection is much simpler than full scan and tamper tags and other such electronics are being developed and deployed by the industries involved. By end of this year, we will have 100% capability of nuke screening internally. Thats just building a sensor grid at the offload dock.
Companies that have huge infrastructure requiring container transit (WalMart, Home Depot) already have security on the ground in SE Asia that verify contents and seals of all their cargo pre-shipment.