Some monsters are illogically (un)affected by mindcraft
Some monsters can or cannot be hurt via mindcraft, despite their intelligence (or lack thereof).
There are monsters that are illogically unaffected by mindcraft, and others that are affected despite having no mind.
The following monsters are immune, and it feels they shouldn't be.
* giant ant worker (other ants are affected)
* giant bee worker (other bees are affected)
* moloch (greater molochs are affected)
* eternal guardian (he can't be considered mindless)
The following monsters are not immune, and it feels they should be.
* gelatinous cube (mindless jelly)
* will o'wisp (floating light)
* gibbering mouther (mindless jelly)
* living wall (mindless wall)
* wall beast (mindless wall)
How to reproduce it
Attempt to use mindcraft on the monsters listed above and notice the reactions.
A complete list can be found here. Testing was done by wishing for all monsters in the game and attacking them with Mind Blast. For uniques, hacked figurines were used.
The living wall flavor text establishes that they have tentacles, ooze paralyzing liquid and possess teeth - nowhere does it say they are mindless. (The D&D living wall, which is in many ways different from the ADOM one, has an alignment of chaotic evil - and you need to have a mind to be anything but neutral.)
Wall beasts are a) beasts, which as far as I know is a term preserved for living creatures (sometimes used as a synonym for "wild animal", I think), and b) have subtle muscles and veins running through them under a layer of dirt, which should be hallmarks of a living being. Once more, nowhere does the flavor text say they are mindless. I'm fairly sure wall beasts aren't even vulnerable to construct slaying.
Gibbering mouthers aren't jelly in the way stuff like gray oozes are - they are an aberration, not a construct, cobbled together out of living things by evil magic, but still have a conscious, albeit a mad one. At least that's what the Wikipedia article on the D&D creature suggests. Once more, the ADOM flavor text doesn't state anywhere that the gibbering mouther is a mindless being. A neat addition to the game might be to add a risk of getting confused by touching the thoroughly mad mind of a gibbering mouther.
Will o'Wisps are evil spirits, most of what they are IS mind. It doesn't have to think in the way humans do, or even be alive. (After all, the soul bound to service in the form of a skeleton can also be affected by mindcraft.) The flavor text establishes that they lure prey into dangerous places to prey on their life force as they die, and once more, nowhere that they are mindless. They appear as a floating light, but if that were all there is, they wouldn't be monsters!
Gelatinous cubes are truly mindless according to the D&D source material, so that might be a simple oversight. The flavor text doesn't say one or the other, though, so it's not impossible to imagine that in Ancardia, gelatinous cubes do have a mind, the evidence being that they can be affected by mindcraft. Who are we to dictate otherwise?
Queens being affected by mindcraft rings true with me. The warriors, I agree that they should be mindless, since I don't really see why they should have more of a mind than claw bugs and such.
I think the idea behind bees and ants is their minds are too primitive to be affected. Dogs and cats are intelligent enough and similar to humans that a mindcrafter can make sense out of it.
Animated Trees are affected by mindcraft. It doesn't make much sense in the light of the above, but it's a nice perk for mindcrafters. They can launch Confusion Wave once completely surrounded by hostile trees and still escape. Add an item or two for regeneration and you don't have much to fear from the forest, because Confusion Wave recharges fast enough to keep trees confused most of the time. It has the downside of making trees hostile and creating traffic jams on your way back, but that's another matter.
Only plants (and missed them in two places but fixed this now), unliving and undead are immune to mind craft. Otherwise it's a function of intelligence and e.g. gelatinous cubes are rated as dumb (but not mindless).
Not so sure about the Eternal Guardian. He's a unique in more ways than one; specifically, he's not only a crowned Champion of Balance, but one that's been tasked with a very specialized mission, and his god has granted him divine powers that they obviously don't give to "normal" crowned champions for the purpose of accomplishing that task (for example, he's apparently ageless, and he can replicate himself). It's not inconceivable that he might have such tremendous willpower as to repel mental attacks (I'd think it'd take a lot of willpower to guard a staircase 24/7 for hundreds of years) or even divine protection from such attacks.
I am posting here to confirm that gelatinous cubes are still affected by mindcraft.
Ghosts are not affected by mindcraft, but it hardly seems they are mindless. At least the monster memory for ghost lords states how they command undead in death now. Seems somewhat hard to do if you're not even capable of thought.