I believe that the main reason for Vintage Ludwigs having mismatched interiors, (some where resocote, some bare and some varnish, sometimes all in the one kit, as I'm sure you know) was simply because some shells had imperfections so the coatings smoothed out the surface of the shells which were "rough" so to speak.
I would say it's up to you whether you varnish the bare drums or not, there is no real right thing to do, I mean they are your drums after all. If it were me, I would just leave them as they are, I'm sure they sound fantastic and the original spec. of the kit would remain intact without any varnish.
I am looking for a vintage Ludwig kit like yours but it seems they are becoming increasingly hard to find in the UK. Do you know of anywahere where I could find one?
Cheers