I think we should, and here's why: If any measure that is ostensibly aimed at preventing terrorism is justified, whether or not it actually prevents terrorism, simply because some people believe it will prevent terrorism, we might as well forget about our constitutional rights and start lining up behind Eve Holbrook.
While we're at it, Commissioner Kelly has another suggestion for how we can make things easier for the police. "Ideally," he told the Times, "people wouldn't carry any backpacks or bulky packages on the transit system." But even a bag-free subway would be vulnerable to explosives strapped to terrorists' bodies. So ideally, people wouldn't wear any clothing on the transit system.

Compared to those ideas, it may seem a small thing to open your backpack, briefcase or purse for what will probably be a cursory examination by a bored police officer. And that is precisely the problem: We are getting used to the idea that suspicionless searches of our personal belongings are no big deal.
As I read the relevant Supreme Court decisions, if the police said they would be randomly searching bags for drugs, unlicensed guns, or other contraband, mentioning in passing that of course they would also arrest anyone they happened to find with a bomb, the searches would be unconstitutional. But since they've said they are randomly searching bags for bombs, mentioning in passing that of course they will also arrest anyone found with drugs, an unlicensed gun, or other contraband, the searches probably will be upheld.
In theory, the courts are supposed to consider not only the purpose of the searches but the extent to which they serve that purpose. In practice, however, judges are likely to be as deferential to the police as Eve Holbrook.