While I am a firm believer in logic reasoning, we also have to realize its shortcomings. The shortcomings stem from the fact that it is our brain that is used to draw the inferences and causal chains that lead to our logical conclusions.
Therefore, when our brain is missing information, or just failing to piece together relevant causal chains, it is easy for it to come to the wrong conclusions.
Your 9/11 reasoning is a good example why you just can't blindly rely on logic, without being extra careful you are not using the shortest, cheapest, and least information dense causal chain (i.e. drawing too simple conclusion, because of lack of information which lead to lack of complex reasoning).
Let me present you with another causal chain that is equally "logical", but requires you to realize you have a complex causal network to decode, instead of the simple a-b-c 9/11-Bush-WMD reasoning you just used.
Let's say the Bush family wanted a war in the middle east. To start that war, an event was needed to unite the US population and steer the public opinion in order to further this agenda.
What has happened since 9/11 in the middle east? A new enemy was constructed; "The Terrorists", and Irak, Syria, Kuwait, Afghanistan etc....has become a war zone.
Did they need to plant WMDs in Iraq to start these wars?
Did they need to plant WMDs in Iraq to start the Iraq invasion?
Answer is no. They got what they wanted anyway.
Therefore, to say that planting WMDs was a requirement for 9/11 "conspiracies" to be true, is just not a valid conclusion.
I'm not saying that what I described above is what happened, I'm just pointing out that the logical reasoning you just used is far too simple, and does not take into account complex causal relationships that may be at work.
Such complex causal relationships only reveal themselves after you dig deep enough into all the available information.
So the problem of blindly relying on logical reasoning for decision making, is the failure to understand that lack of sufficient information can still lead to incorrect assumptions.
https://www.youtube.com/watch?v=9RC1Mepk_Sw&t=1m03s
In many cases it has been shown that conspiracies turn out to be true. And instead of the simple causal chains people believe that can be used to refute the conspiracies, it turns out that what you need to understand everything is not a simple chain, but something much more complex instead.
I like to call these complex things not causal chains, but causal networks. That is where the real logic brainwork starts.