Towers and fortresses are gone forever when killed. This is intentional, to keep the game from going back and forth indefinately. (or at least a long time)

Rook can indeed spawn towers, but they are weaker, limited in number and temporary. (they disappear after a while, or when an additional tower is built over the current limit)

That's provided that the wall segment still exists to support it. IE, if you have a Tower of Light, wall segment, and an empty tower spot that eventually spawns an Archer Tower with sufficient war rank, if you destroy that Tower of Light the entire wall segment is gone and the Archer Tower will never be created.

While you can't replace lost towers, there are citadel upgrades to give them more health and health regen, and also to deal more damage (including splash damage) to make them more dangerous.

At the stages of the game where you have 30,000 gold to spend, nuking a tower is effortless

you can heal towers for 2000 using the Universal Gadget, Hard to tell wheter or not its worth it though..