As a frequent international traveler, I feel naive here... can anyone point out any resources as to why this is best practice? What's on the line here, and what's going on that we need to be aware of?
For any company that has external NDA obligations, this seems like a no-brainer to make legal compliance very easy. You don't want to disclose your proprietary company data, well then make a policy that says don't put proprietary company data in a position where it is likely to be subject to legal searches without any strong requirement for a warrant (probably a very short list of situations, maybe just when passing through Customs.) Now you can sign NDAs and pass through customs too, and don't worry about any potential that a conflict between the two could put you in a precarious legal position.
Customs has very broad legal latitude to perform invasive searches on a whim. (Here in the US, I don't think I even need to pass through customs to be subjected to invasive searches like this when passing through an airport.)