It will create a null Pointer Exception.
Setting a boolean with empty will get you something like "Null pointer exception, boolean cannot be set to null" if the flow gets to the exclusive split you will see an error in the server console log something like "Null pointer exceptionNo outgoing document defined".
You can prevent this by checking for !=empty first
Stephan Bruijnis is correct if you create an object in a way where you can actually leave the boolean empty, or if you apply entity access and you cannot read the boolean attribute at all an error will occur.
However, if you use a default pattern by creating an object and not assigning a specific value to the boolean attribute + the user has access it will just follow the path of the default value you have set on when defining the attribute. Which will also be the value that gets saved if you commit.