Yes, I really don't get that.

The inventory doesn't pause because realistically it shouldn't, and because inventory pause would take away some of the tension in the game. You're still not really expected to be running around while looking in your inventory. If you need to look around, you'd just close it.

There's only one mouse; if you have it controlling the cursor, you can't have it controlling the view as well.
Using keys to navigate the inventory would make it much harder to use.

I don't see what the alternative would be. Switching the mouse to a cursor while in inventory/meu mode is pretty much standard for any game with an inventory, other than strange edge cases like Thief or Hexen which generally only have very few items.