My pet peeve is publications spelling NASA as Nasa. They've come up with some story to explain their decision that sounds just as bad as some of the lies Walter White told. I don't care how ubiquitous NASA maybe, it is and always will be an acronym. I accept removing the dots so it's not N.A.S.A., but I will only accept Nasa as a formal name if that's the name of a person.
How do you feel about "scuba" or "laser?" Acronyms that are pronounced like they're spelled (eg, Nasa, gif, taser) tend to end up being spelled like words sooner or later instead of being in all caps.
Personally, I don't write SCUBA or scuba, as it's just not part of my day to day conversation, but I would go with SCUBA. Also, it's never just laser or LASER, it's friggin LASER!!! Pew Pew!