The point of EGR is to suck in burned fuel mixture to slow the combustion of the regular air/fuel mix. Slowing the combustion lowers the temps and creates less NOx. Some vehicles can suffer spark knock after disconnecting the EGR, but it's not common on 2Fs, because the compression isn't very high to begin with. You can leave all the equipment in place (for a visual) and plug off the manifold port, if you want. If you have removed the EGR vacuum line, the EGR will not open and exhaust will not flow through that tube.
If I were desmogging, I would put a BB in the EGR line, be sure the EGR valve is actually shut, and cap off that rear manifold port, to prevent current and future leaks. Many people cap it off by dropping a slug of steel in there and welding it in place. You can then bolt the tube right back up and it will look stock/OEM.
Steve H. - KE0KNH
Colo Springs, CO
'78 FJ40, '89 FJ62, '98 4Runner