Hydrocortisone cream works to get rid of warts. Just put some on the wart each day
Warts are a virus and as your horse's body builds an immunity to the virus, the warts will disappear of their own accord, so dont worry about them :)
Magnesium deficiency might make a horse more vulnerable but if you add Magnesium you also need to know in what state - Magnesium, Magnesium Orotate, ... the list goes on.
If the warts are causing a problem, ie in the corner of the mouth and being irritated by the bit, use PODOPHYLLIN (purchase from Chemist) to paint onto the lesion. Do not 'torture' the horse with other "remedies".