TL;DR Bonita: Generic, all-purpose term for "pretty" (and sometimes "beautiful"). As a case in point, the film Pretty Woman was translated into Spanish as Mujer bonita. Though there are many types of beauty, this word appears to be referring to a woman's outward appearance, especially if she is thin and graceful.
El DLE define la niña bonita como 1. f. Especialmente en los sorteos, número quince. ¿Cuál es el origen de este modismo?
One of your assumptions is incorrect. In Mexico, at least, bonita would be fine for a female but bonito would only be okay for a boy. It would be a complicated word to use for a grown man -- in general it would be best to avoid it for a grown man.
I read in the RAE that niño bonito/niña bonita was an expression. What does it mean exactly and what is the etymology or the origin of this expression?
1 "está" is the 3rd. person, singular of the verb "estar". In English: "is". "esta" is a pronoun, it translates to "this". Esta casa está inclinada. Esta linea está torcida. Esta mañana está muy bonita.
1 Por ejemplo, cuando evitamos el uso excesivo de palabras que sustituyen a los nombres, como "cosa (s)". En lugar de decir: "esta cosa está bonita", decir "esta taza está bonita". En ese caso, preferimos llamar al objeto por su nombre. A esa acción me gustaría saber si tiene algún nombre y cuál es.
The verb ver can be used in a few different constructions to convey how something looks or seems: Te ves bonita. Se te ve mal. Te veo bien. For the reflexive constructions, the WordReference entry ...