In MySQL Workbench (at least, in 6.0) they are also using Scintilla component for editing SQL, and they somehow manage to differentiate such SQL features as major keywords (CREATE, SELECT, UPDATE, etc.), and functions. Especially those keywords, when highlighted, make huge positive difference. Unfortunately, there is no configuration panel for the Workbench editor colors (and default settings suck), but there is a file named code_editor.xml, in which it is possible to change those colors (color settings are mine).
<style id="7" fore-color="#A6E22E" back-color="#272822" /> <!-- SCE_MYSQL_MAJORKEYWORD --> <style id="15" fore-color="#66D9EF" back-color="#272822" /> <!-- SCE_MYSQL_FUNCTION -->
It would be great, if also Notepad++ could support those syntax elements. I know, it could be difficult, because it probably needs to change all themes, but the change is worth it.