I can't guess why HDTV went with that number system but as your cable company has total control over this, the order, lineup in not a mystery. They did it.
As to channels, you are doing far better that most Comcast today as Comcast removed all Clear QAM OTA channels.
http://www.tomsguide.com/forum/54273-4-comcast-pulls-1080i-free-channels for example.
The move accelerated with many reasons why. One of them are customers that complained of missing channels. With a cable company supplied tuner, they can control what comes in and warrant it.
My tv is connected up to my cable provider with a typical coaxial cable. We're having an issue though, where the channels display as decimals. 44.532 is an example of a channel we get. They are in a different order than what is normal with this provider in the area, for example the channels for cable in one stretch go Cartoon Network > Nick > TVLand > Comedy Central > USA > TBS > TNT but the order here is totally different.
The other major problem is that we dont receive probably over half of the channels that we should be getting.
Any advice on what's going on?