If there were 3 shots in quick succession, and if the first shot hit her in the head, then she's not going to scream. The bigger issue for me is how much time elapsed between him yelling at the intruder, him getting the gun and him shooting. After he yelled, if she was really in the bathroom, wouldn't she had said something then or even poked her head out to see what was going on?
Did she hear him yell about an intruder and her first inclination was to lock the door so that the intruder wouldn't get to her, not knowing he was actually yelling at her?
The biggest question, and the one that will ultimately cost him, is why he felt the need to blindly shoot at the door without ever verifying who (if anyone) was in the bathroom? Whether he purposely attacked her or his story is 100% accurate, there is no explanation for him to just blinding go shooting a gun in his house without never even actually seeing a person in his house. I know there are a lot of gun owners who stand by the fact that if they see anyone in their house they are going to shoot first and ask questions later. But in his own account, he doesn't even verify that there is someone in his house. He sees an open window, hears a noise, and just started shooting. On top of that, he never ever verifies that Reeva is in bed. There are two people in the house, you know that, someones in the bathroom, shouldn't you at least check if the other person is using the bathroom?
I'm like a lot of others, I want to believe him because I can see a scenario of why someone would be so scared due to their lack of legs, plus the environment that they live in. But you have to stretch your mind to either a) his mind was compromised, b) he's an incredibly paranoid individual, way more than normal and c) he has no common sense.