Webdriver utilizes a browser's native support for mapping the DOM element to WebElement object using id/xpath etc.
The JavascriptExecutor.executeScript
executes an external script in the context of the currently selected browser window. (similar to an augmented browsing tool like grease monkey, if you ever used),
and in case the script returns any DOM element its converted into WebElement object.
One can also say, the click simulated by WebDriver on a browser is similar to what actual user do as compared to one invoked using javascript.
In reality, with WebDriver not all the events can be automated flawlessly with all the web browsers, in fact with different versions of the same Web browser also. (i.e. different version of IE, FF etc behave differently). Still WebDriver is the near best tool available for this.
Once (~4 years back) on a certain version of IE we observed that we can't send right click or may be hover mouse on generated menu links, so we used js to simulate that, which performed very much browser independent way. so you can now conclude what executing external javascript can be good for.
Also, there are automated web testing frameworks which use javascript for everything instead of browser's native support. e.g. :http://en.wikipedia.org/wiki/Sahi_%28software%29
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