I'm near the endgame now (doing the 3 main light path quests).

Some things I've noticed about enchantments now that I have a GM Water enchanter:

-I often find or enchant +16 Dodge on items, but nothing similar for armor skills
-I often find/enchant +16 Unarmed, but nothing similar for weapon skills
-I often find/enchant Stealing, Disarm Trap, ID Item, ID Monster, Alchemy, but never saw any other skills! For example no Perception, Bodybuilding, Merchant...
-I sometimes find (but never managed to enchant) Armsmaster on items
-I very rarely find rings that give +50% to a magic skill. Rarer than relics though. I have 3 so far, and 6 relics.

Basically Monks are the biggest physical combat beneficiary of enchantments, and you can get away with not GMing Disarm Trap/ID Item because you'll get a huge +16 boost.

Side note: how annoying is ID Item? They force you to move the item to the character who has the skill to be able to ID an item, resulting in a lot of time wasted on inventory management. I fired my scholar once I GMed the skill, then one dungeon later when I realized how annoying this is, had to spend like 20 minutes trying to find another scholar to hire him back. Waste of skill points. Why couldn't they make it convenient like the Scholar?

monks get pretty crazy in the late game with this, I don't think bodybuilding merchant buffs exist even when you aren't enchanting yourself.

also kinda offtopic but I don't remember if you could pull "of darkness" enchants with enchant item, n if you could is it more common with master or gm water?

Some enchants are simply more common than others, as you'll have already noticed. That said, I don't know which skills are eligible for a bonus via enchantment.

Scholars are super convenient, though an Instructor/Teacher combo gives more XP. Also, while it isn't a big deal (for most parties) by that point, there's one dungeon where you won't have a scholar.

One way around it is to just have your ID Item character scan everything in a chest before you take it out. I don't know that it is much more inconvenient than some of the other "One character per party skills", like Repair Item, Disarm Trap, Merchant, or Alchemy. I think "Of Darkness" requires GM Water; I'm pretty sure I've had it happen a handful of times over the years. It is rare, though.

M&MVII seems to keep some skill enhancements to just NCO's

NPC's--- not corporals