The word so far seems to be that the Arbiter will accompany the Chief on certain missions; as such, it may be assumed that he is invulnerable, or else he may disappear from the game before completion.
Other NPCs that accompany the player through the game will not be invincible.
UPDATE: No. Most of Halo 3's features are known at this point. Bots are not in the game.
This always gets asked. Bungie hasn't ever done a multiplayer game with bots. It's conceivable, I suppose, but not at all likely.
UPDATE: The below was written in early 2007. Approximately two months before release, Bungie announced that Halo 3 will feature cooperative play via split screen (two players per box) as well as system link and Xbox Live (four players per game). In a four-player game, the host players the Master Chief, and the other players are the Arbiter and two other Elite warriors.
Any combination can be used; four players can use separate consoles over XBL or system link; two players can share a box and connect to players on one or two other separate boxes.