Be prepared when you pull up those deck boards to end up replacing a few. Not sure what style yours is, but most are open on the bottom so they will have some rot and you will break the joint when you pull them up. A local tractor trailer supply store will have the kind you need, or you can rip your own on a table saw. I'd much prefer to buy new ones if you can find them.
If you really need to go thru the trouble of pulling the deck boards to access the rusty spots, you might as well add a splash screen below the decks and insulate on top of it, like a 5th wheel. I've never had a box that didn't get a little damp from the underside in bad weather. I'd go with something like 2" - 3" pink foam board, then closed cell foam around the cut and cobble so it's fairly watertight, then your water barrier material below that.