Hi Brandon - short answer, the probe on the USB model is the newer, full spectrum, version which is supposed to have a more even response curve that could provide some additional accuracy for our lighting systems. I don't think anyone has done a direct side-by-side comparison on the two units with any of our own lighting setups to confirm this however (thought about it) so it's unclear how large of an effect it might have. You are also correct in that the USB model requires you to download an application (see original post for some details) onto your computer (limited Mac support) in order to utilize it. As long as you have a supported OS, it is pretty straighforward but it does require that extra step (and a computer). The hand-held is the older probe but it is an all-in-one solution - just don't drop it in your tank!
Hope this helps.