I would advise if it is not absolutely unavoidable to remove the cones to leave them be. Only if you have to replace the nuts or have leaking cones, then it is worth doing. And any time when reusing old cones, use liberal dub of pipe goop to seal. And bubble test. Always do bubble tests as soon there is an opportunity.
The reason is that the 45ci intake manifold is thin as a blade at the spigots and as the cones are of brass, the nut has to be tightened hard in order to clamp and seal, and that distorts the thin spigots. Add to that the expansion and contraction from the cylinder heat and vibrations does wear a groove in the spigots, even more so if the carburetor is unsupported.
Never ride with a unsupported carburetor, some version Scouts did not have that from factory. Make a support if there is none. It is danger both from fire hazard of a sagging leaking carb, and risk of engine seizure from air leaks.
As the spigots are thin, there is little to no material to turn off to make a smooth surface for new cones, so it is almost always needed adding material (hard solder brass) or cut off entirely and make new tubes to press in the manifold body. 37ci manifold spigots can be a bit thicker but do wear in the same way.
So restoration of the spigots is problematic but that is almost always needed if old brass cones are removed as their position is altered and they become distorted, and especially if they are replaced for new because new cones are really difficult to get to seal in the grooves that the old cones has made...
If a decision to restore the spigots is made and the spigot surfaces are round and smooth then, is what I think is best, to use the new plastic cones that is reusable and does not require the nuts to be torqued as hard in order to seal safely. If used on rough surfaces they don't always seal well.
