I forget who the author of The Atlantic Wire article is, but the article's headline is misleading and the conclusion drawn from the facts, that a person can use the NSA trademark without fear, is wrong.
Trademark law centers on consumer confusion.
Good parodies will not confuse. Whether a parody is a good one or not can often be left for a court to decide, however, if the trademark holder is not fond of the use of the mark.
If an average consumer could mistakenly but legitimately believe that a tee shirt using a NSA seal was an official tee shirt of a NSA agent or sponsored or endorsed by the NSA, you can almost bet on the tee shirt maker (and, potentially, the wearer of the shirt, depending on facts) facing more than just a nod and a smile from NSA.
With the "Smokey the Bear" trademark disputes - one wound up in court with the parodist the victor; the other has resulted so far in a notice of infringement and a demand to cease and desist the use of the Smokey trademark on "anti-fracking" products, but no suit has been filed as of yet against the creator of the products (to my knowledge).
As to the use of the initials NSA for the National Shopping Association, there would be little chance of confusing one with the other - at least, I would hope

- so the National Security Agency would have a hard time preventing the use (unless the shopping association made NSA products with the intent to deceive a consumer into believing there was a security agency connection). There are, for example, several ABCs that are used without problem.
Using the
name "National Security Agency" on a product, on the other hand, could be a clearer no-no.