I'm averse to all caps in general and italics as emphasis. There is a reason why some publishers expect manuscript submission in plain text. You need italics only if you give the title of a book or words in a foreign language, i.e. in literary writing all mark-up is formal, not prosodic.
If you want to show that direct speech is being shouted, you can say so, or use an exclamation mark:
- "Where is she?" John shouted and grabbed the front of my shirt.
- John grabbed the front of my shirt. "Where is she!"
Sentence structure makes it clear that the second version is a question, so a question mark is not necessary.
I prefer the second version over the first because of show-don't-tell.
3 . John looked at me confused. "Where is she?!"
I understand the third version to mean that the speaker is surprised and not necessarily speaking very loud, while the second version means he is shouting.