If you don't ask for encrypted files, you get the FST gui. If you want encrypted downloads, you add -dlEncrypted to your command line. That gives you the .app and .h3 files that you'd install with WUPInstaller.
I'm not sure what distinction you're making between 'regular' encrypted downloads and eShop. The titles that you're downloading from the NUS server are all eShop, and if you're going to install them with WUPInstaller, you want them to still be encrypted.
One thing you have to keep in mind with JNUSTool is that it makes no effort to create or obtain a ticket for you if there isn't already one in the title on the NUS server. You have to get a real ticket from that ticket site (for games that are available on disc), or create a fake one using the TitleID and NUS key that are on that same site. If you need help with creating tickets, you should ask in a different thread, since that wouldn't have anything to do with JNUSTool. (look for funkiiu)