Yes, if you get attacked the bot will try to activate the shield generator if it can. It also takes other defensive actions like using up all resources on an attacked planet so an attacker can't steal them.

By default the bot will prioritize buildings that provide resources, then depots, then shipyard & mission control skill. It will also build explorers and start launching explore missions once the shipyard reaches level 13. Upon request, we can enable combat ship mode, which will throw all resources into producing warships and prioritize that over buildings.

Also, the bot will use all your mission control slots, but we can set it to leave a number of missions free upon request, so you can manually launch some missions.