The mook is a feature of many campaigns and genres. They are basically there to die to make the heroes look good. The classic example is the Star Wars Stormtrooper, feared across the galaxy and only able to hit one frigging target in six movies (also they hit the only woman in the SW galaxy the fiends!) Also I think the armor was designed to attract blaster bolts to the chest to avoid costly medical bills.
If you don't simply want a horde of mooks to make the heroes look good you have to do a little work to figure out WHY they're a horde of suck. In most space operas the reason is that they simply propel the plot forward. No matter how bad they shoot there is a great number of them an eventualy you'll have to run.
Many referees have a problem with letting characters waltz through opposition. I'm one of them. There is some justification for mookishness in Terran history allowing a smaller force to fight its way to glory or survive to fight another day. Here are some popular reasons for being a mook.
1) Inept leadership. There is a saying that incompetence rises to meet its level. Maybe your superior got his job through relatives or a caste structure or kissing up. For whatever reason he's awful. Examples: Any group, anywhere, anytime has a couple of them.
"Order an all out attack."
"Sir that didn't work the first 16 times."
"Exactly. No one would expect us to try it a 17th time. We'll have the benefit of surprise!"
2) Inappropriate tactics. The British regulars were taught to fight in file and row to maximize their firepower. Other 18th century European armies behaved similarly. When they engaged the American colonials they were shocked at the way the rebels ducked behind trees and shot at individuals. Similarly the great armor superiority the Third Reich enjoyed in the invasion of France was due to their massing their tanks at areas of attack. They achieved local superiority even though the French armor exceeded theirs in quantity and quality.
"Have the armor form a defensive line to our rear so we have someplace to fall back to!"
"Do you expect us to retreat then?"
"Based on the last 17 frontal assaults the anecdotal evidence supports me."
3) Equipment issues. This is a catch all also covering tech levels. If your enemy has iron armor and weapons and you still have copper equipment it's just not a fair fight. Similarly if they have laser blades that shear through your armor then congrats, you are the newest resident of Mook-ville.
"The news from the front is bad. The alien invaders are centuries ahead of us in technology. They tipped their arrows with some kind of shiny hard stuff that goes right through our hide armor!"
4) Biology. Maybe you're a nocturnal subsurface dwelling carnivore being drafted to fight in daylight. Maybe you're from a planet with a thicker atmosphere or (different proportion of oxygen). No one can really blame you for missing, can they?
"How could you all miss?!"
5) Psychology. This is the most subtle reason for failure and one the mooks may never realize (in other words it's good for a long term campaign.) At the risk of straying too far off topic the classic example is the Tolkein's orcs. One on one they could give a human a good fight. The problem was getting the miserable curs to work together for any length of time, let alone fight as a unit. It might not take an act of God but it took at least an act of a god. If an orc met a human alone odds were the human was screwed (humans were not all soldiers after all.) If twenty orcs met twenty humans it was an even fight (at twilight or dawn at least, see #4). If 100 humans met 500 orcs the humans would rout them them (barring undead wraiths on pteranodons because undead and dinosaurs are just too epic). In the Traveller setting Vargr and Aslan might both suffer from this difficulty, ignoring orders and tactics to seek personal glory or satisfy their honor.
"Nyaaaaah. Hey Aslans, you're drawn completely wrong!! You look like terriers!"
"HU-man ape! Pilot close on that starfighter! Prepare to fire meson cannon!"
Last orders of the commander of the Aslan dreadnought Fithhtythadzvgrrrry before slamming into 17 space mines.
All this brings me to two important points about using mooks.
Every good mook has at least one area they are good at, even better than the good guys. Maybe they have crappy starships but they excel at trailing your ship or setting up ambushes. Maybe they are lousy fighters but great spies and assassins. You need something they can do to be a problem to your characters' way of life.
"So he's a great fighter, this pirate captain?"
"No, he's a dog shit. That's why he's very careful not to ever hit a free trader when the patrol is around. We never even caught a scan of him."
Mooks are made not born. No one has a genetic code marking them as a mook. Realistically all these poor bastards have good reasons for being mooks. All these reasons can be worked around. Maybe the crappy leader has food poisoning and his brilliant long frustrated aide leads this attack. Every mook has his day. Maybe they trip over their own feet 95% of the time but that other 5% will make everything seem worthwhile.
"Do those troopers have new sights on their laser rifles? Run!"