You are trying to compare two different things. You have less of a problem if you start with:
1. Why do you think he stole the money?
2. How do you think he stole the money?
#1 can be interpreted as:
a. Why is it that you think that he stole the money?
b. Why did he steal the money, do you think?
#2 can be interpreted as:
a. How is it that you think that he stole the money? (admittedly very unlikely, but possible)
b. How did he steal the money, do you think?
Now move on to:
3. Why do you know he stole the money?
4. How do you know he stole the money?
Neither is ambiguous - only one interpretation is possible. Admittedly, #3 is very unlikely, but it's just about possible.

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