I'll take a stab at it Ernie...
The short answer is ..sometimes. It depends how the engine control system is set up, and the the case of EEC-IV, it sees the lack of EGR manifested in higher combustion chamber temps, because the recirculation of exhaust gases lowers chamber temps to thwart the formation of NoX (nitrogen oxides) emissions. So...the chamber temps run hotter, introducing the possibility and tendency towards detonation, and the computer will then pull timing , and also run rich, affecting performance and fuel economy.
Most of the time, you wouldn't notice a drastic change, as the computer does it's job. Other times, like yours , she spits out codes complaining about it. Every car is a bit different (even SC's of differing years respond differently.
Sometimes the better choice people make is to allow the EEC to "think" it's working by putting a plate in betweeen the manifold and valve, instead of just plugging the vac line. Let it work as normal. Of course, this still affects combustion chamber temps, and timing may be pulled, but the system , including the feedback transducers, will not throw codes (ostensibly).
Hope this helps, you really need someone that has been through exactly your scenario, with your year of SC, to give you some more insight on things you can do. Good luck.