Most scanners recently manufactured will monitor the control channel and direct the scanner to the voice frequency automatically. Only early models required you to enter all the voice frequencies.
Almost all scanners now support "control channel" only operation.
That being said, it would not be unusual for all frequencies (control, alternate, and voice) to be loaded based on downloads or other ways of programming simply because some old radios still require voice frequencies entered.
There is no issue with having these voice channels programmed in the radio. Most will work without them and they do not slow scanning speed because the radio only monitors the control channel anyway.
I usually program all frequencies of a system.
It is not impossible for a system administrator to reassign a voice channel as a control or alternate control. If this would happen you would no longer get control channel direction to true voice frequencies and no longer hear the system.
