[DNSB]

If you are using KOReader and not sending the books to a location accessible by Nickel (see the excluded folders item (in .kobo/Kobo/Kobo eReader.conf, look for the [FeatureSettings] header and under it, ExcludeSyncFolders=\\.(?!kobo|adobe).*? for example.), Nickel is not able to access the books and it will not import them to the database.

Again, this comes down to where you are copying the books to. If you are using only KOReader to read, why bother sending kepubs since only Nickel will make use of the extra spans and so on. Perhaps not using the KoboTouch driver and using the generic driver instead would be better suited to your purposes.