Its a hostile Galaxy ;-)

The EEM Mod is actually not about building large Capitals and stuff, its about exploring the Galaxy filled with stuff.
The spawn algorythm is completely Random so you might have the 'luck' of using a seed on your world that spawns a hell of content, most of the Time People are complaining that there is not much to nearly nothing that spawns, so many People would call you lucky for experiencing this overload.
As the spawnrate is Random, there's not much you can do about it but building continuesly ammo for your ships (or use Laser Turrets that don't require ammo) and win the fight.

No worries at all about the hostilities. I expected more than just a few bad guys. The building the large capital was just me trying to get my feet on the ground so I could begin exploring with a husk of a ship that needs supplies.

If I'm just unlucky, then perhaps I'll just disable the mod until I have more than just gataling guns on small ships. :3 I still think the concept is super cool, and I plan on re-enabling it again soon. (That and the ships I've fought are pretty cool.)

I've never seen the projection shield before though, I'm thinking the mod also adds new items. Is there a guide or anything for the mod?

I noticed the frequency too.
Also, those drones won't fly in moon's gravity. You can hide there if possible, until you get your ship armed. Just watch it so they won't crash-land on your head.
BTW, is that projection thing actually a sheild, or is it just for camouflage?

Haha, that's actually unexpected xD The more people play EEM, the more interesting situations can occur, what you describe is more like stucking in pirate sector in x3 terran conflic/albion prelude xD And there pirates were jerks as well - attacking your biggest and most vulnerable crafts (like when you just captured corvette and it's without weapons and shields and you need to escort it from this hell) :D
Anyway, did they just come out of nowhere or may be pirate station spawned nearby? If second (or you can clearly see any hostile antennas which can spawn pirates nearby) - just relocate, leaving antenna radius. If they called by pirate scout V-9 that haunts you all the time - well, then that's my fault, too frequent spawnrate of those scouts... However, when you know exactly how those spawn antennas work, you can prevent reinforcements really quick by destroying antenna - there's a timer for first spawn, after you entered antenna radius, mostly it's 30-60 secs

About projection shield - that's just for distraction and it's vanilla, create similar shield out of armor blocks, save as blueprint and put it into projector