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We can directly use a clause whose first word is "that" as a single entry. For instance,
- "That she is pretty does not ensure that she is kind."
While on the other hand, we also say
- "How is it that she shouted?"
Since a clause whose first word is "that" can be used as a single object, as exemplified in (1), I am strongly tempted to simply say "How is that she shouts" instead of (2), can I? If not, why?
"How is it that she shouted" is a bit of a strange sentence. "how is it that" is an expression, and it basically asks how something works or how something is possible.
For example:
So your example sentence sounds like it's incomplete, like you wanted to say something like
How is it that she shouted when she was barely even whispering?
That's an example of someone saying "your friend shouted" when your friend was actually speaking quietly, so in effect you're asking "when someone is speaking quietly, how is that an example of shouting?"
Otherwise, just "how is it that she shouted" implies that she shouldn't have been able to shout (for example, she underwent throat surgery), so you wonder how she was able to shout anyway. If that's your intended meaning, sorry for the above long explanation :)
Since "how is it that" is an expression, you can't just drop the "it".
