I'm getting ready to do the final painting on my 109 boat in 1/72. In most of the pictures I've seen there is almost no rust. That's because unlike steel ships the crew could get to just about everywhere. Places where you might want to add some very light rust is around guard rails. But again just a hint. More corrosion can be done around the exhausts.
I'm planning on doing some pre shading under the torpedo tubes, in the cockpit areas, etc. where you would find shadows. Then I'm planning on doing some post shading to replicate the natural fading from the sun. My dilemma is how to account for the wear on the decks. If you look at photos of these boats the paint often is worn off in high traffic areas. For example from between both sides of the cockpit to the bit on the foredeck. I'm trying to decide if I want to use a wash, or if I want to put down a primer coat, top coat, and use a fiberglass eraser to remove some of the paint and then add a wash. The primers on these boats were described to me as "yellow" which makes me think it might have been some sort of chromate. I'm imagining that yellow being slightly visible from the wear. Again, I could achieve that with some wash too. Still practicing with that before I do the final paint job.
You said 1/48 scale? The only kit I'm familiar with in that scale is the Bluejacket model. It's made from wood which provides some different opportunities for weathering. For example wear down the final paint and stain the wood. That would look very cool. I've been working on my Bluejacket kit since... well, let's just say it's been a long time. I'm hoping to finish that one up this winter. Here are some photos of it in progress...
In this picture you can see what I mean about the wear on the foredeck.
Here are some photos from the guys at Royal Model. These are photos of the Italeri 1/35 Elco. They did some very nice weathering effects on this boat.
And finally my 109 ready for the paint shop...
I hope that helps.
Good luck with your project.
Dave