I'm wondering about this, because even though I've cut off the soldiers' access to food, money, and weapons, they don't seem to be substantially more dangerous or easier to kill than before. Is the "weakening" a purely cosmetic thing?

Soldiers are indeed much easier to kill, and do a lot less damage.

Well, maybe it's just me, but I didn't see any great differences. Especially during that one scene were my weapons were taken except for my starter pistol, where it would have been most helpful for the enemies to be weaker.

Well that would be because the soldiers you're facing at the end are elite soldiers (red shirts), so they're tough even if you did weaken them.
Weakening the soldiers is most useful to do as early as possible in the game, so that you'll have an easier time with white and yellow shirt-soldiers.
The end-game is meant to be hard, otherwise it wouldn't be any fun. My main problem with it is that I almost ran out of ammo. I literally killed the end boss with my next to last bullet.

...but the process of weakening all the soldiers means you've already probably crossed all the maps and killed most of them. Hardly seems worth the bother, at that rate...