The Moebian Sixth Guards turning traitor to worship Nurgle makes a lot of sense, as part of their motivation for doing so was feeling neglected and forgotten by the Imperium despite going through a lot of trauma in battle for them. This of course sows strong emotions of hopelessness and despair — emotions that Nurgle embodies.
Further, what Nurgle brings to the table is a logistician's dream. The ability to easily deny and contest resources to enemies by spreading disease, turning enemies into cannon fodder to preserve their own forces, and severely reducing the need for medical supplies makes Nurgle rather appealing (compared to the other Chaos Gods) to a force perpetually fighting an uphill battle with a focus on their own preservation.
The players opposing the cultists and Moebian Sixth traitors have Toughness, described in the Overview Trailer as the determination to press on through the pain. This directly contrasts hopelessness and despair, which is fitting in their fight against Nurgle. Furthermore, the enemies lack the players' depletable but regenerating Toughness, but have Armor instead — a static value that represents the stagnation of Nurgle.
In canon, the Poxwalkers' groans are enough to infect the souls of victims with the Walking-Pox, except the most faithful Imperial citizens. This likely explains why the Poxwalkers' infectious groans don't affect your characters — as established in the game's cutscenes, they're very faithful to the Imperium's cause.
One voice line for the Zealot, "Blood for the Emperor, Skulls for the Golden Throne", may at first glance seem wildly out of place being called by a loyal agent of the Imperium fighting against Chaos. But despite also opposing the Emperor, Khorne is not always on the same side as Nurgle, either. It's not out of the question (and indeed, he has done it before, against Magnus The Red) that Khorne might lend a little bit of His power even to a servant of the Anathema, if it lets Khorne get a little bit over Nurgle in the Chaos Gods' Great Game.
Indeed, this has happened in canon, more than once. In addition to Khorne empowering Logan Grimnar's axe Morkai, the novelization for the Fire Warrior game flat out states that the protagonist Kais is empowered by Khorne the entire time, even screaming the Khornate warcry at one point.
When it comes to gun-wielding Scab and Dreg enemies, there are Scab Stalkers, Scab Shooters, Scab Shotgunners, Scab Gunners, Scab Snipers, Dreg Stalkers, Dreg Shotgunners and Dreg Gunners, but no Dreg Shooters or Snipers. Shooters and especially Snipers are longer-ranged enemies compared to Stalkers and Shotgunners, and the Scabs were former guardsmen, thus having more well-trained aim than the Dreg cultists who were civilian converts. Dreg Gunners, despite being long-ranged too, do exist as their weapons' fast-fire rate offsets their less-trained aim.
The Pox Hounds in levels with the Hunting Grounds condition are spawned in large numbers but are weaker than standard Pox Hounds, with less health, are more prone to being knocked off by attacks, and will even eventually let go of a player they have pounced on without needing to be attacked. It can be assumed that areas with the Hunting Grounds condition are where Pox Hounds are trained up to become the more dangerous and relentless standard variants.
Why do the Guard use codenames for the various enemies they come across? While it could be that they are a standardized form of identification that could be used across the galaxy, it could also be a layer of mental protection. The use of codenames serves to further dehumanize the foes they face and thus make it both easier for them to kill without a thought and also for them not to be traumatized by their work.
The Veteran having more Toughness than the other three classes (even more so than the Tank-like Ogryn) might seem odd at first glance, but it actually makes sense. One of the best known qualities of The Imperial Guard/Astra Militarium is the fact they are a Red Shirt Army that can send thousands if not millions of soldiers to their deaths in a single battle. For someone to have reached the status of Veteran, they would have needed to be as tough as nails in order to survive the sort of horrors that would have killed an average Guardsman in seconds. The other three classes may be Tough, but they're simply not as determined to serve the Emperor as the Veteran is.
Furthermore, the Veteran is the most disciplined and combat trained of the classes, and a big part of combat training is learning the difference between being injured and merely being in pain. The Zealot and Ogryn have more Health to represent having their intense faith and abhuman durability respectively to fall back on to push through serious injury, but the Veteran is much better at knowing how to properly respond to pain and injury and thus can handle the accumulation of minor damage much better, especially since they're unlikely to make things worse by trying to ignore an injury that they shouldn't. The Psyker meanwhile is implied to be unaccustomed to walking long distances let alone actual combat, so naturally the Psyker has the worst Toughness AND Health.
Also, mechanically, while the Ogryn does have less Toughness than the Veteran, he also has by far the strongest toughness recovery skills in combat, able to recover a hit to their toughness bar and be back at full within a second or two of taking a hit in melee. On the other hand, the Veteran's higher max bar size enables you to better handle taking a few shots and then ducking behind cover to recuperate and then repeating the process.
Each class has a base Stamina value that is added to the Stamina of whatever weapon or object they have out. Since Psykers are non combatants pressed in to service, they naturally have the lowest, and Ogryn being superhuman gives them the highest, but it initially seems odd that the Veteran has a slightly lower value than the Zealot since the Veteran is trained to endure long marches. However, it makes sense when you consider that running out of Stamina doesn't stop you from doing actions that require Stamina, it just reduces the effectiveness. A Veteran has lower Stamina because they're trained to preserve their strength for the long haul while a Zealot is running themselves ragged on pure adrenaline and is likely much worse for wear after each mission. This is even reflected in their Talents Trees, since the Veteran's Stamina based Talents are more about improving Stamina management while the Zealots are more about operating with depleted Stamina.
In the first Carnival mission Hadron uses a vox jammer to screw with the Sixth's communications, but in the second mission someone uses a vox jammer to screw with yours. The Morrow/Rannick chatter shows how this must have happened - Rannick's lack of surprise at the vox experiencing 'unexpected' interference during an ambush combined with him immediately suspecting sabotage even when Morrow himself dismissed it implies he knew it was going to happen, meaning the Traitor stole the vox jammer from Hadron in between the two missions and Rannick was waiting to see when it would turn up again.
