Imo, don't apply a cost to remove second kitchen as an adjustment. Applying cost to cure as an adjustment is bad methodlogy, because it does not result in an "as is" value, it would result in an "as repaired" value, and most likely your client wants an as is appraisal.
You can provide a cost to cure estimate on addendum, don't mix it into the sales grid as an adjustment.
Describe and photograph exactly what is there. Don't play games and call it a kitchenette or finsihed space or the like. If it is a second kitchen, it is a second kitchen.
It is the lender's call if they want to lend on a home with two kitchens, or not.
If there are no permits for it, then state that as well. If you can find out local zoning code if it is legally permissable or not, then put that information in. Usually a deed itself will not have a restriction against a second kitchen.
Re, in the sales grids, if you can't find comps with non permitted kitchens, imo, it is best to show no value for it. If it is not permitted, it has no resale value because typically in a purchase appraisal the lender would want it taken out. It might have personal value to those using it, but proving resale value is different.