Hi Benni.
When you say a 'natural' varnish, do you mean just a clear varnish to protect the wood etc? (Doh! I just re-read the title of your post!

)
If so I would recommend an eggshell or satin clear for the hull sides and a matt one for the decks.
Although I have used some good acrylic varnishes, I've found personally that the spirit based best quality ones such as Ronseal give the best and smoothest finish on the wood, (saying that I've never tried airbrushing acrylics so they might be better that way) don't forget though that water based varnish is like painting your PVA'd planks with a solvent, it
shouldn't affect the glue, but there's always a first time!
I generally brush varnished my ships with a good quality soft haired brush about size 6 to 9 or so and if your'e not spraying it on, work on smaller sub sections at a time, eg the hull below the bottom wale, stern section, one or two gun decks etc. Once its dried check for rough areas and if required give them a light sanding with fine grade wet and dry (used dry normally), wipe off the dust with a rag then give another coat.
Sounds complicated but its not that bad really. The time to do it is now, as you thought, its a nightmare to varnish smoothly once the details start blocking up everywhere!
Best of luck and post up some pics when you've finished!
Robin
First wooden ship:
The Grimsby 12 Gun 'Frigate' by Constructo Second:
Bounty DelPrado Part Works Third:
HMS Victory DelPrado Part Works 1/100 scale
Diorama of the Battle of the Brandywine from the American Revolutionary War Diorama of the Battle of New Falkland (unfinished sci-fi), Great War Centenary Diorama of the Messines Ridge Assault
Index for the Victory diary is on page 1