This depends a lot on the vehicle, or specifically the generation. Newer vehicles (late model, OBD2-post '96) vehicles are computer controlled. Let's look at the purpose of the Exhaust Gas Recirculation Valve. The EGR does as its name implies, it recirculates exhaust gas containing unburned hydrocarbons (fuel) to reduce harmful emissions. Engines will run hotter with less gas (lean) and cooler with more gas (rich). The computer accounts for the EGR, without it the engine will essentially run leaner and hotter. The pcm would have to be reprogrammed or flashed to add fuel to make up for the lack of EGR. Most mechanical alterations to late model vehicles also require pcm reflashes in order to run properly.
I'm guessing that the performance manifolds you've seen without EGR ports are for older, non-computer controlled engines, carbureted engines. EGR valves on these engines always hindered performance partly because they were added on to old engine designs that weren't originally made for an EGR. These types of EGR valves were also completely mechanically controlled and weren't very accurate or efficient. They also couldn't account for carb setup and ignition timing like a late model computer controlled fuel-injected distributor-less ignition engine.