Windows tools are a lot faster, more reliable, not prone to errors on the disc, and you don't have to burn DVDs. If you have backups/originals that you don't have the ISO of and they work fine from the disc, they should 95% of the time dump fine with the USB Loader. If they don't dump fine, the USB Loader will freeze, forcing you to reboot the wii. It won't show up in the game list, but it will still eat up space on the USB HDD.
I would recommend you to download ISOs of any discs you have that still have torrents with a decent amount of seeds, and dump the rest of your existing discs using the USB Loader.
For future games, obviously download ISOs and use the windows tools to add them to the USB HDD, it's faster and more reliable.