When Notepad++ highlights a document, it considers lines to be equally spaced, regardless of their contents. As a result, the line spacing is based on the tallest font that was specified in any element of the style settings for a given language and a given theme.
If you think there is too much space between lines, chances are that a font was specified for something that is not being displayed and which is taller than the fonts used for what is being displayed.
To guard against this, it might be a good idea to use the same font size across all the settings for a language. Also remember that fonts with bold weight are slightly taller than normal fonts.