Considering the impotance that cooling towers are to power plants including nuclear ones, they represent a vunerability. Unfriendly nations with precision munitions or suicide bombers flying explosive laden aircraft could create havoc by entering the cooling tower from its large opening at the top. It seems only prudent to consider the need for a convex shaped dome to be placed on top as protection against such threats.
In most cases a dome sufficiently curved to cause deflection of impact would suffice. Air flow could be maintained by placing smaller multiple holes in the top or around the rim.
Retrofitting existing towers could be done with segmented parts and helicopters.