I also have this problem. I recently started collecting 1/1200-1/1250 models, and found out the hard way that the larger models (cruisers, BBs, CVs, etc.) are big, heavy lead weights that try constantly to break free and bounce around inside the box during transport like a loose cannon. Proper storage is critical, but I agree a good varnish coat is important.
I treat the DDs and other small/light vessels (esp. resin models) like any other miniature I've ever painted, and just use a hard gloss coat then overcoat it with spray mat. Like John Leahy I have started using Windsor and Newton Professional Matte spray, because I consider it pretty much equivalent to Testors Dullcote.
I've only done one of the big ships (USS Enterprise), and I followed the same procedure for her. The details on a 1/1250 Neptun model aren't really any smaller or more subtle than buttons/rivets/lace on a 15mm soldier, or panel lines on a 1/200 scale aircraft, or the hyperdetailed sculpting on a GHQ model, and I use the same spray technique for all of those.
I think I would agree that it would be easy to brush on a clearcoat too thick. It depends on the clear coat product (some are thicker than others), but I have actually encountered that problem. I've never suffered detail-filling with my usual spray clearcoats; usually dry pretty thin if applied correctly, and if applied incorrectly there are worse problems (runs, drips, orange peel, crackle, etc.).
- Ix
PS: There are spray clearcoats labeled "triple thick" which definitely fill in detail, on purpose. Don't use one of those. 
dips his toe into the Russo-Japanese War.
