Im not sure what you mean,are you referring to Ve Pro when you say 'only 16 instruments per instance'? because One Ve Pro instance can load 512 instruments,thats 32 ports with 16 midi channels per port.)
Are you confusing ports with channels in Protools midi tracks outs?

I use Protools 8 and when I click on the midi tracks outs I can see all the ports,at the moment im only using about 4 ports = 64 instruments in one instance of Ve pro,

In each Protools midi track when you click on midi out you should see (for example) 16 VE pro ports and when you click on each port you have a choice of 16 midi channels.

hoe this helps,]Dean.