For the example's sake, lets try to add in a filter that optionally gives me the Shield component

I was not working with filters by myself yet, but as I can see from the #[system] documentation you can only apply filters to a single query (when the system is defined with #[system(for_each)] or #[system(par_for_each)]). The example you provided attempts to work with two different queries at the same time, and the #[system] macro does not have a way to describe filters in that case.

I managed to do it like this:

#[system]
fn beam_array_damage_update(
	targets: &mut Query<(Entity, &mut Hull, Option<&mut Shield>)>, 
	sender: &mut Query<(&BeamArray, &TargetingConsole)>, 
	world: &mut SubWorld,
	#[resource] dt: &DeltaTime
) {
	...
}

I didn't know this was even a thing, until I read this issue and the amethyst docs linked in it.

But as you said for a complex filter my solution probably won't work.