bracco, nice build. And I think the weathering on the deck, especially around the metal hatch covers, looks great. It's going to be a great model when finished.
I too like to use a brush, rather than an airbrush, for military models (except of course where you need a fuzzy blend of colours for specific camo patterns) because it helps with the weathering process.
Specifically, on painting my U-boat, I made all the brush strokes on the topsides in a vertical direction. While the first stroke might have been any direction to get into corners, before it can dry I always brush it in the direction that rain and any other elements would cause streaking.
Even if you can't see the brush strokes yourself, when you do overcoats for weathering, the next colour will tend to pick up slight differences in the brush marks and enhance the weathering effect.
The other comment I can make is not to dispair on your waterline. In fact, USE it!! The white markings I see (from tape pulling off?) can be used to increase the weathering, it's almost exactly where some rust would show up and where algae would build up on the hull. But the way it's happened on your boat looks entirely natural, just not the correct colours.
So when you get around to doing the weathering, try and get the rust/algae colours that you're using to cover the white parts, rather than trying to paint more grey there. You could even build up layers because in real life, the algae is on top of the paint. Also keep in mind that the anti-fouling paint below the waterline keeps the algae and rust away longer than the topsides paint, which is for camo and therefore doesn't have the antifouling ingredients mixed in.
Also, don't worry about the Naxos too much. If you're patient enough to wait for 203 months, you can get a replacement part sent from the kit manufacturer. Just email them.
OR, you can scratch build a Naxos that will look more realistic than the kit one anyway if you have the skills. Your local hobby shop will have brass rod/wire of the right thickness, or you can use efine electrical wirer without the plastic insulation. (I always save any scrapes from a telephone repair for instance, those thin wires are VERY useful). You can make the mesh to go around it from fine screens, like what comes with gasoline can filters, or some kitchen sieves. For the two little antenna on the Naxos I'm using whiskers from my cats. (No, I didn't pull them off, they fall off every once in a while and I always save them) The cat's whiskers are thin enough but unlike wire, they don't take a permanent bend when bumped and they will stay in place if you predrill a hole in the wire and/or CA them in place.