There is no other way of sorting channels. The system was tailored to ATSC where each channel has channel number added to the from of the name automatically. I actually have an opposite problem from yours. When I use cable channels, I wish to be able to sort channels by name, so I can find a particular channel (it took me a long time to remember that HBO is on channel 186), but cable channels also have channel number in the front automatically.
With regard to the duplicate channels with (1) at the end, they are not caused by having dual tuners. You do not need to scan for channels with each one of the dual tuners, but if you did, no duplicate channels would be created. The channels with (1) at the end are the same channel but different audio stream (in UK they are audio notes for visually impaired). It is still on my list of things to do to revamping this scheme, but I am not sure when I will be able to get to it. For now you need to select all of those "(1)" channels and hide them (not delete them! because they will come back if you ever need to re-scan).