First, don't let it intimidate you. Rules can smell your fear, and use it against you.
Most NPCs should not need much in the way of updates. If you have not yet visited the Wizards web site, go there and get the 3.5 Accessory Update PDF. It presents the upates for some of Wizards' own books to 3.5, but it also neatly lists most of the changes. It is a very good tool for getting a handle on what needs to be updated.
Most NPCs will work pretty much "as is"; they may not be 100% 3.5 accurate, but for most gaming, 90-95 % is close enough. The things to look out for are spells that changed. If a new spell is based on an old spell that changed, THAT would need to be adjusted. Take Emotion, for example. Some Cleric domains included emotion. The spell is gone in 3.5, replaced with individual spells for some of the effects (and the others are just gone).
Second, nothing HAS to be updated. So that Emotion spell can be used as it was in 3.0 as a "special" spell in your world.
The designers have made the comment that people could be playing a mix of 3.0 and 3.5 in the same game and not realize it for a while. Depending on the game being run, this could well be accurate.
The point is, though, don't agonize over it. A 3.0 book is still quite usable in 3.5, generally. Check the publisher's web sites for updates occasionally, though. It never hurts to have the information.