If I start a Service 3 times while it is already running, do I have to call stopService 3 times to make it stop?
No. One stopService() is sufficient.
I know it's not a good practice to do so
Sure it is. If desired, your activity (or whatever is calling startService()) can blindly call startService() without knowing or caring whether the service is up and running. For example, if you are implementing an IntentService for handling downloads of mid-sized files, the activity can call startService() for as many downloads as the user wants. Note though that IntentService stops itself when it has no more work to do.