My take on it is that she's projecting a little bit in the versions where she has the ''Diana Prince'' secret identity in some capacity. She is Diana of Themyscera, known to the world as Wonder Woman, and sees ''Diana Prince'' as merely a cover. She probably thinks the same is true of Superman - that's he's really Kal-El of Krypton and ''Clark Kent'' is just a cover.

Quote Originally Posted by Mysterious View Post
She did it in Justice League movie too
Quote Originally Posted by DABellWrites View Post
Which was the weirdest thing ever, like... He had just learned he was an alien and barely used it or others called him Kal-El. Did you even expect him to respond to that name?
It made sense there. In the DCEU, the whole world knew that Superman's name was Kal-El...in fact he was known as Kal-El before the name ''Superman'' was ever a thing! Also, Diana never really got to meet Clark Kent, unlike Bruce. She only met Superman/Kal-El.

Quote Originally Posted by Restingvoice View Post
I'm going with the interpretation that Diana uses Kal because they're both immigrants while Bruce calls him Clark because they're both raised Americans.
That's a good take. Likewise it makes sense for J'onn to call him Kal-El, while Barry, Hal etc. call him Clark.