SOS is a case in point. SOS is just SOS. It is most definitely not S.O.S.
SOS is a Morse Code prosign. Like all prosigns, it doesn't stand for the individual letters. The letters are just a way of writing out the sound. SOS definitely doesn't stand for "Save Our Ships" - it was first introduced in Germany!
In Morse code, the letter S is "dit dit dit" and the letter O is "dah dah dah". When you send individual letters, you pause in between. So if you were sending the individual letters S O S, or a word that happened to be spelled "sos", you'd send "dit dit dit <pause> dah dah dah <pause> dit dit dit".
But that's not how you send SOS. You run it all together: "dit dit dit dah dah dah dit dit dit".
The same is true for other prosigns such as AR which means "end of message". The letter A is "dit dah" and the letter R is "dit dah dit". But you don't send AR as "dit dah <pause> dit dah dit". It's "dit dah dit dah dit".
If someone sent me the individual letters A and R with the pause in between, I wouldn't recognize it as an end of transmission. I'm listening for the entire sound of "dit dah dit dah dit". It's really more like a big long "letter" of its own.
Prosigns are customarily written with a bar above the letters to show that they are connected without a pause. Of course, that's not always possible, but they definitely are never written with dots between the letters.
Except in New York, where they love the periods no matter how wrong they are!