The lead copy editor at The New York Times, Merill Perlman, explains in a Q&A why the paper abbreviates the Health Insurance Portability and Accountability Act as Hipaa rather than HIPAA:

“The New York Times Manual of Style and Usage” … calls for any acronym of more than four letters to be rendered with only the first letter capitalized, thus Hipaa. One reason, as you can see, is that an all-capitalized acronym calls attention to itself, possibly distracting a reader.

This is probably also why the AP Stylebook mandates Nasdaq instead of NASDAQ, something I’ve gotten used to over time. Hipaa will always look strange to me though.

I have never really thought about it this way before, but AP and New York Times style manuals focus a lot of energy on making copy as streamlined as possible, so the eye moves smoothly across the page without a lot of undue interruptions. Newspaper editorial style is like the original usability design.

Perlman also clarifies that HIPAA is a true acronym (because you say the abbreviation as a word), a common mistake that people make:

Let’s not confuse an acronym with an initialism, like F.B.I. Both are formed from the first letter in each word, but in an initialism the letters are pronounced individually.