Assuming they are iron or mild steel bolts, it won't do any harm, but don't expect it to do much good, either. The rust is unlikely to affect your ability to get the nuts off when you replace the bolts - the nut usually has to come off with a cold chisel anyway!
Mirellie must have had probs with keel bolts. But the nut will come off, wire brush it, soak it in WD40 (or parrafin) then try a large socket. If no luck try large "stillsons wrench" + scafold pole, then plus larger pole, even in tight spaces like my "Folkboat" the nuts will shift.
If you want to "pull" the bolt for suveys ect. Take the nut to your local Marine Engineer (I/m lucky I live in Fraserburgh) and get him to give you another nut + bolt of same thread. Screw new bolt through new nut and half of old bolt onto new nut and keel bolt. Hit top of new bolt with "force" if keel bolt does not move use larger "hammer" it does work.
Keel bolts do turn into thin bits of nothing. The main problem seems to the reaction of steel (mild or wrought. iron)........wrought is best but costs lots of money, with oak.....forget stainless, its rubbish..... but thats another thread, stainless needs to breath (to erode) to survive, shut it up as a keel bolt and it will fail before mild steel.
10 bolts in 3 1/4 ton iron keel, each bolt 1 1/4" diameter. Bolts replaced every 12 years, so twice whilst I've owned her.
Score: Nut undone by above methods: maybe 8 or 9
Nut smashed with cold chisel: maybe 11 or 12
You won't be re-using the old nut, so if it won't shift fairly readily, you may as well cut it off, I reckon, rather than waste time on it!
The "Really Important Thing" is not to allow the bolt to waste and to "neck" between the wood keel and the iron keel - regular replacement indicated. But if I look at the Wooden Boat website, I find that Americans seldom replace keel bolts!
