IIRC the NYTimes at least used to have a policy where it if you pronounce the acronym out loud as a word it doesn't get periods, but does have periods if it would be said out loud as individual letters. E.g., "Joint NASA - E.S.A. space mission launch", "F.B.I. agents meet at FEMA office". As far as that rule would be concerned SOS is pronounced as letters and not as a word perhaps like "sauce".

But I've just seen some clear violations of that rule by them (they don't spell "SAT" test with periods) so maybe I'm misremembering or maybe they've changed it. Similarly to SOS, the letters SAT don't stand for anything, at least not officially anymore.