[RPG] Do all creatures have souls

It doesn't say it counts as armor or natural armor or anything, so it doesn't. It's just 1 AC on top of everything else, to emphasize the sturdiness of Warforged. It should stack with everything and prohibit nothing.

To support this, note that the Warforged trait provides a bonus to AC, rather than setting it to a number, as armor is wont to do. The Tortle, another race with an armor-related ability, sets its armor class to 17 like armor usually does, and correspondingly disallows further benefits from wearing armor, further illustrating that abilities that provide bonuses to the class of worn armor (like the Warforged trait) are not armor and are intended to modify armor, while abilities that provide a different default armor class probably count as armor and definitely don't modify the effective class of worn armor.

Sure, it can.

It is a bit crazy! But everything wizards do at that level is a bit crazy.

A 14th-level necromancer is, like, Sauron-tier. The point of being someone like that is precisely to call up terrible minions from the grave and terrorize the land with them. The Nightwalker is a great fit for the role of "big dumb undead minion" rather than being a boss in its own right.

What most DMs do to prevent the game from breaking is to simply not play at 14th level.

If one of your PCs is a necromancer, and you throw a Nightwalker at them, then the player wrangling the monster and yelling "Yee-haw!" from its back while they stomp around is probably the exact outcome you expect.