LOL, that's very odd about the rats screaming dunmer battle cries. That's either a very odd mod conflict, or the guards from the vault are nearby on the other side of the wall and trying to help you kill them. Also, the rats are an essential part of your tamed nix-hound diet.
Just open up their cages near the dungeon entrance and they'll come running whenever they hear a rat nibbling on your shoes. It's actually pretty entertaining watching them go (The runt of the litter Nixxy won't fight though, just fyi so nobody thinks he's bugged). I don't even bother engaging the rats anymore, I just let the hounds play with them as I walk away chuckling.
I upped the rats on the encounter table and decreased the number of random adventurers rampaging through the dungeon for the sake of realism, and also to make the occasional random intruder more exciting rather than, "ho hum, another orc, bosmer, whatever in my dungeon...sigh..."
Spoiler There's a hidden hole in your dungeon, which explains how rats, and thieves keep getting in.
Also, the intruders won't be dropping any ebony armor. They wear mostly crap, though some of them have random loot tables so there's no telling what odd mismatched piece of armor might be in their inventory. It's a low level loot table though, so you probably won't see anything good drop off of them. They're there to spice up the dungeon, not be free loot vending machines.
I didn't personally place any ebony weapons in the mod, but I'm sure there were some lying around the tower from the original un-modded stronghold, which I didn't remove. There might still be some left over from Uvirith Inside as well, which served as base for this mod, though it's now hardly recognizable. I don't remember it adding any though. I remember when first playing the game, I raided Tel Uvirith (as Hlaalu) and found all that ebony loot and thought "Score!" Now I get my tower with free ebony longswords and think, "sigh, another unsellable piece of encumberance that I have absolutely no use for as a mage." Yeah, they really thought that through.
I didn't remove anything from the original tower though, just shifted it around and added new stuff, just so it wouldn't dirty unmodded saves.
The trapdoor won't open until you find the key for it, which turns up later as you do some quests given by the prison warden.