I use sildur's enhanced shaders, whenever I enter the sludgeon when the shaders on, there are clones on my screen, braziers are glitched, lens holes are visible through blocks.

That's caused by Optifine or your shaders. Some of our renderers depend on certain rendering features that Optifine/shaders break or disable. Not much we can do about that unfortunately.

I'm not currently using Optifine or by extension shaders, and am currently experiencing this odd issue as well.
Are there any mods known to cause this besides Optifine?

I can also see the tunnel effect that worms emerge from through the vast majority of blocks:

Seems like ShootIt was causing the problem, some way, somehow.
EDIT: Not entirely, something's making the fog interact weirdly, so I can't see the braziers in the crystal without standing behind them.
Will keep hunting.
EDIT 2: Okay, I don't know what changed, but I'm not able to reproduce this issue outside of my actual survival world.
EDIT 3: Finally got it; it was ArmorChroma, and it only affects the crystal when you're wearing a piece of enchanted armor. Weird!

NOPE!
I got ahead of myself; the issue is with enchanted armor period.
Most likely something weird with trying to render the player's enchanted armor (Possibly other items as well) in the crystal.