'No, it doesn't' is the abbreviated version of 'No, it doesn't mean that there will be no investigation of the accident.' Since the two speakers know what A is asking, there is no need to repeat everything after 'doesn't'. B is correcting A's apparent confusion as to whether or not there will be an investigation. B could also have said simply 'No, there will be an investigation.'
This slight difficulty in responding when there is more than one negative involved arises quite often. 'Is it true that you are not going to stop denying your lies?'
To deal with this, we often add a comment to our reply, to clarify it. 'Yes, I will not stop denying this'. Al