Two possibles here - just warm air or actual exhaust?
A picture of the hole in the exhaust manifold and what/where those tubes were connected would sure clear things up.
When the hole on the exhaust manifold has nothing in it - is it an exhaust leak where you get exhaust blowing out? Or is it just warm air from a choke stove? It could be just a cavity in the exhaust manifold to heat up air to operate the choke.
Or, if the hole goes all the way into actual exhaust, it could be for the EGR. Yes, recycling a SMALL amount of exhaust back into the intake does lower the combustion temperatures. That's how/why EGR valves and floor jets work.
The exhaust is an inert gas, supposedly it no longer has oxygen or fuel in it - if the engine's running right. It's not unlike Helium, it does nothing but take up space. Recycled back into the intake, it spaces the HC and O2 molecules slightly apart, lowering combustion temps. But only a little bit is needed, too much radically affects performance - downward.
When the combustion temp gets lowered a little, below about 3000 degrees. 3000 degrees is about where Nitrogen gets welded to Oxygen, forming Oxides of Nitrogen (NOx,) - deadly gasses that cause smog.
Now reality - many folks just don't understand what they have, many folks modify or drill things out, thinking they are improving things. That's not always the case, but the previous owner may have.
Take a few pics of what you have, and tell us what comes out of the hole in the exhaust manifold when it's unplugged. Then we can help better.
Hopefully there is no real pressure that comes out of the hole, then it's simply a warm air "stove" to heat up the choke.
Yes, there are plugs available for flared fittings. Go somewhere they have a good assortment of fittings. Or you can just fold and pinch off the tube, or solder/braze/weld it shut.