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You don't need to have the services stopped to perform the copy; however, if there are users in the system, it could cause you problems. The App Copy utility performs a Database level application copy. If data changes occur while the copy is occurring, you may not get those changes as they could be cached in server memory. It's also possible that tables will be locked due to actions performed by users in the system which will cause the Copy App to fail. (You will be able to restart the failed table copy; however) The source database could incur a performance hit while the copy is being performed; however, if you avoid peak periods, this shouldn't be a problem.
Also keep in mind that, this all depends on what you are trying to do with the copied app. If you are making a copy to test a change to historical data, it won't matter if you miss some cached data.
It should also be noted that you can control the copy process. Under the Advaned tab, you can limit the copy to specific Years or Scenarios. If you only need 1 year's worth of data, why copy everything? This will also greatly minimize the tables that need copying lessening the chances of any data contention issues. You can also Filter invalid Calc Status, Data, or Zero value records; however, this will be slow things down and require more resources from the database server.
Hope this helps.