True, the Unnatural abilities are not necessarily the best idea. I'll agree with you. It's not a flaw specific to Deathwatch, but a flaw to the entire 40k RPG system. They're honestly kind of stuck with it, though, ever since DH.
As pointed out by others, it really does represent that the sheer volume of attacks is allowing a chance that a small amount of damage will be done. It's not that an individual knife does more damage, but that the greater number of attacks allows the possibility that one strike will hit the ***** in the armor, or that the multitudinous repeated blows at a single location might cause some bruising/damage or weak spot, etc.
"Average" folks *can* be enemies/opponents of a PC team. Why not? Say there's a rebellion on a planet that the killteam is on. A hundred men with autoguns are a threat that needs to be eliminated/taken care of. Now, they probably aren't as much of a threat as a lascannon or two ... and they won't be with the Horde rules either, but they could cause some minor damage to the SM if left unchecked.
From what I can tell, DW will tend to have a mix of enemies:
Horde "minions" or troops, and single dangerous opponents.
Single dangerous opponents would vary from Orks to Genestealers to Named NPCs. Horde minions, in various sizes, are the troops at their disposal. Whether this is PDF troopers, a ragtag mob of urchins, a pack of wolves, or a bunch of termagaunts, etc.
Yes, Hordes are probably for the most part used as obstacles to slow or wear away at the SM, rather than primary enemies. You might, however, encounter a situation where 4 or 5 Hordes accompany 1 or 2 single enemies (their leaders, for example).
I totally agree that this is mostly opinion, and you are perfectly allowed/reasonable to be cautious. I'm not saying you're wrong or anything like that. I just wanted to point out what I thought about the Horde rules as I understand them (from the brief snippet in the free RPG book), to try to alleviate your (and anyone elses) concerns. As a GM, it seems to me it will make larger-scale combats easier, while also allowing for the GM to throw less exotic foes against the SM and still have them provide some sort of threat and ability to delay the PCs.
The Horde rules seem to be a reasonable method to keep the high-powered/epic feel of SM while allowing the use of more 'average' foes as a credible threat (in sufficient size).
One thing I didn't mention, and to keep in mind, is that a Horde is (usually) somewhat fragile and its morale can Break due to casualties, and causing it to run away. So, your SM can wade into a mob, slaying dozens, and the mob might eventually run in fear from your uber-ness. Epic.