The rust on the dowel nuts won't have any effect on their strength, they'll be absolutely fine to keep using. If you don't want them looking rusty, just pop them in a tub/glass/bowl, fill with Coke and leave for a couple of days. If you do want to buy more, I just get mine from Screwfix. They've been out in the shed for ages and show no signs of rusting.

In terms of battery and ESC boxes, do you have any spare plastic left over? It wouldn't take much to knock up a couple of enclosures out of offcuts, as well as fashioning a lid/restraint for them. Alternatively, just grab some plywood and wood screws from B&Q, will probably cost about the same as if you were to buy a commercial solution.