My impression is that your issue is related to not using the VST3 version of VEP.
So the 16 MIDI channels (per 'port') is a limitation of MIDI nobody can do anything about. But you can use multiple ports, and VEP is capable of handling (according to manual: 32 MIDI ports, on page 45 VSL, needs to be updated) 48 MIDI ports with 16 MIDI channels each, thus a 768 MIDI channels in total within a single VEP instance.
In Cubase, when you set-up you VST instrument, make sure you look for the VEP VST3 version in your 64-bit plugin folder. You should see two different VEP versions, one labeled "x64", which happens to be the VST2 version. Pick the other one (yes, counterintuitive, (http://community.vsl.co.at/forums/t/34658.aspx). Now you should be able to access up to the 48 ports x 16 MIDI ch each. Hope this helps.