I'm not sure what the actual possibility of new interchanges being built is in the foreseeable future. I know some people around Buffalo were calling for something at Youngs Road (no potential to duplicate) a while back, but I'm not sure the Thruway is actually interested.
Again, I definitely don't see the need for signage to have prefixes/suffixes with this. There is NO continuous ticket system down the mainline and Berkshire Spur the way there used to be. There are no less than six: NYC-Albany/MA, Albany-Syracuse, West Syracuse, Syracuse-Rochester, Rochester-Buffalo, and Buffalo-PA. MassDOT may aggregate toll gantries into a single charge, but NYSTA does not. In any case, I could see using suffixes like E or N to differentiate on bills to make them more clear, but I don't see why that would need to extend to signage.