I actually use the Apogee 64 card and have nevered used usb mode with my Symphony. My understanding is that the Symphony I/O is limited to 16 channels in Usb mode, so most likely Cubase(or other DAWs) will only be able to see those 16 channels only.
With the Symphony 64 Pcie card you would be able to run up to 64 channels in any DAW that supports that amount.
Like I mentioned before, I can use Cubase, Logic , PT HD 12 all with this card.
I believe you can use Pro Tools HDX with Cubase but you wont be able to use the dedicated HDX DSP within Cubase. I’m sure you can find more on this by searching google or better yet, gearslutz.
Your best bet would be to try out a Trial of Cubase and test out with your current setup to see how things work for you.