My understanding is that Netbeans directory deployment is simply that...copying files to the directory.
I don't use it for EARs because the current version of Netbeans is simply way to slow on Windows. The bug is fixed, but they haven't released an update yet as far as I know.
But with WAR deploys, again, it's simply a directory update. But Netbeans is "smart" in that it "knows" when it can simply copy files, and when it has to restart the application. For example, if only JSPs change, then simply copying files will work. But if you change a class, you need to redeploy the application.
Either way, it's an incremental copy, but sometimes it has to redeploy the app no matter what.
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