The heat shrink sleeving idea should serve although I don’t entirely like the idea of opening out the holes.
If you are determined however it might be an idea to put a thin smear of my favourite rust stopper, wool fat, on the studs and then shrink the sleeving over that. The sleeving will hold the wool fat in reducing any small tendency for it to contaminate the water spaces and at the same time filling any small voids under the sleeving. Polishing the studs to as high a finish as possible will also serve to delay the onset of corrosion.
Alternatively how about painting the studs with a quality two-pack paint? The studs should be prepared by sandblasting if possible to give a really good key.
Another possibility is coating them with an epoxy resin, (Araldite), again sandblasting would be needed for a good bond.
The trick is, as best as is possible, to electrically decouple the studs from the rest of the engine, the dissimilar metals plus the water are effectively a battery so any insulation of the surface of the studs will help.