My general rule with NPCs is that some are designated as having some sort of actual agenda beyond being simple mathematical equations, but they tend to be few and far between. This is especially if the game is very lacking and doesn't have much conflict. Usually I keep one or two token major NPCs simply to keep things lively.
My biggest tip with NPCs would be to have them each set to specific percentages of money into... whatever you have to sink money into. It means you can copy/paste their orders more or less each turn, making adjustments to percentages where prudent (an NPC at war will change its percentages to more spending in military fields until the war is over, for example).
My biggest rule of course, is that major NPCs can't use espionage on another major power.
The easiest way to make sure there's no possible NPC abuse is to not read player orders until the end of the turn. If a player has a question, they should send it in a separate PM labeled as such.
Also, should probably avoid IOTChat when you're a GM as much as possible. Something diabolical about it decreases the chance of the next update seeing the light of day because you totally have a new IOT idea that everyone'll love.
The trick is to make them (updates) consistent. Whether small constant updates, large updates once a month (and which you block off an entire weekend for), or whatever in between. Make it a part of your lifecycle, and you'd be more likely to succeed.