Will our missiles be able to lock on to specific points of the larger capital ships such as the engine or cockpit, or will we have to aim them manually?asked by Renji

When it comes to bigger ships, you'll be able to do sub-system or component targeting, and as such you'd be able to lock different kinds of missiles on to those. Perhaps they might be able to lock them onto a gun-turret, so yes, you'll be able to do that.