Galvanising by hot dip gives a thick coating of zinc. Provided air pockets are avoided and cavities done properly it will give the best long term protection. It acts has a double function by making a durable coating and also provides an electrolytic protection method. However, drilling - even widening existing holes - will remove the zinc layer leaving potential for localised corrosion. Any coating removed in this way will also leave a "gap" as they all rely on creating a barrier as the first line of defense. If drilling then its worth trying to replace the removed zinc with something, either the special paints etc. also, after completion of the job, apply another layer of protection - waxoyl/underseal etc.
That takes me back to my metallurgy days!
Even stainless steel can corrode, especially at welds when incorrect filler metal is used as this can create an electrolytic cell which causes corosion on a microscopic level, weakening the weld. If welding s/s then use a filler "stabilized" to remove the effect and a very low carbon content. Its the combination of chrome and carbon that causes the effect known as "weld decay"
sospan