I just completed the rank missions that come after vanaduke (only learned about them now, haven't played much in the last two years), and in the last combat one, with the white levels and black monsters, I found that my ally continually got stuck on the monster spawners, and in the last fight of the last level, instead of warping to me when I started the fight, he warped up above the set of gates that lower one by one, leading to the exit (I tried to screencap this but apparently it didn't work as I was in fullscreen). Additionally, over the course of the three levels, I found exactly one stun vial and no vitapods, pills, or other pickups, which is a little unusual (I found a vitapod at the fourth level treasure chamber, after all the fighting was done). Was any of this normal?
Also, I'm wondering if there would have been any way to disable the black particle effects that pop up randomly and cover enemy attacks.
Yes, that's how it works. Vitapods are very rare (until the treasure level, when you don't need them anymore). Vaelyn is a pretty powerful and dedicated fighter, except that she doesn't help at all in the final fight.
The black particle effects are the Swarm. You can look it up on the wiki. Yes, they make the fight harder, presumably by design. (But it's nothing compared to what the Swarm does in a Shadow Lair.) Swarm effects are present even on the lowest graphics quality, so I doubt that there's any way to disable them.