Yes, you can hide command prompt window now in Selenium 2.40.0. I was writing a blog article about this earlier, which you might want to have a look here.
Please note that hiding command prompt window is not recommended.
ChromeDriver
var driverService = ChromeDriverService.CreateDefaultService();
driverService.HideCommandPromptWindow = true;
var driver = new ChromeDriver(driverService, new ChromeOptions());
InternetExplorerDriver
var driverService = InternetExplorerDriverService.CreateDefaultService();
driverService.HideCommandPromptWindow = true;
var driver = new InternetExplorerDriver(driverService, new InternetExplorerOptions());
PhantomJSDriver
var driverService = PhantomJSDriverService.CreateDefaultService();
driverService.HideCommandPromptWindow = true;
var driver = new PhantomJSDriver(driverService);