Uh - kind of.
If you let whatever coat cure and dry properly then you can varnish with either or version. So if you have done weathering and are happy with it then whatever varnish for whatever effect you want the final to be. So if I am doing a beaten up warbird then I will do a matt varnish, at this point because nothing is going to go on the top of it then it doesn't matter if it is lacquer or water based. As long as the weathering has dried totally then its fine to just cover it in whatever.
If you're painting in enamels, I would prime, do the base colours then coat in gloss (doesnt matter the type lacquer or aqua) do your decals then coat in aqua / acrylic varnish (Alclad Aqua Gloss is the one I use) then do your enamel / oil washes (make sure to use a not so hot thinner or it will still go through the varnish! - I use winsor newton Sansador) then seal with whatever top coat you want, so in short:
Primer
Enamel base coats / shading
whatever gloss coat you have - doesnt matter type generally as long as the base coats have properly dried
Decals
Aqua gloss coat - something like Alclad Aqua Gloss
Weather with enamels and oil washes (note the because you used a water varnish you can not use acrylic washes here!)
Then top coat with whatever effect you want.
Pete