1. No it's not good for the battery. You should never flatten NiMH batteries as it will shorten the life.
2. How long have you waited for the laptop to shut down? Generally there is something running which requires the process to end in cases like this.
You could try this:
1- Start/Run and type Regedit
2- Navigate to HKEY_LOCAL_MACHINE/SYSTEM/CURRENT CONTROL SET/CONTROL
3- Click on “Control” [highlight]
4- Select “Wait to kill service timeout” [in right hand pane]
5- Right click and select “Modify”
6- Set to a lower value than 2000
7- A setting of 200 will be sufficient
I use a setting of 500 which prevents any funny messages at start up for me. You may need to try one or two different settings.