Clash-of-clans – Question regarding COC Wartime troop upgradation

The troops in the clan castle indeed defend each attack.

You can be attacked more than two times in a war, but your clan castle is always full for defending against those attacks, full of whatever was in the castle at the end of the war's preparation phase.

Additionally in war:

1. Heroes are always active to defend your War village.
2. Defenses like Xbows and Inferno towers, and traps are preloaded
3. Any defenses under construction are active in war, unlike your home village. In fact, any defense STARTED prior to the end of preparation day is active and defends your war village.

All defensive towers are active in your war base, even if:

1. They're still being built (Level 0 to 1)
2. Being upgraded (they'll be at the level before the upgrade start)
3. Out of ammo (ie. X-Bows)

Answering your query about newly built towers that haven't been completed yet:
They'll function as normal, they'll be physically there (not leave any gaps) except only as Level 1.
I mean c'mon... Who's seen a Level 0 building?

Note: This only applies to newly built buildings... Or at least those that are under construction.
Cancellation of its construction will remove the building from your War base.