I just use wire brush and poke any compacted mud out of the holes with an old screwdriver. Paint with Hammerite, at least two coats, which is available in loads of colours. Make sure you get the paint to fully cover including nail holes otherwise the rust will appear again.
You need to be wearing eye protection and old clothes for this, as it sends quite a bit of debris flying around. You'll probably want to wear leather gardening gloves, too; if you touch the brush with your skin, it will sting. Quite a lot.
The friction will also warm up the shoe, driving off any moisture.
I don't paint the shoes, but wipe them over with Renaissance Wax; it's expensive stuff, but a little pot goes a long way. There are now other micro-crystalline waxes available (this, for example) that I only learnt about tonight.