As a longtime TiVo user I can't recall any point in time in which getting (and activating) a CableCARD was as easy as getting a set top box. It almost always involved at least a phone call or maybe an online chat.
In store salespeople have been saying they "aren't supported" or "going away" since like 2005.
If you have working cards or can get them via phone call there is probably no reason to worry about it. They will most likely work as long as they continue to support the hundreds of thousands of set top boxes they have in the field with internal CableCARDs.
Once CableCARD support is gone there will be no provider/network supported way to use your own DVR of any sort. As the OP suggested, that would be the end of Channels DVR for cable tv use.
I can't imagine many people would pay a traditional cable provider $80-$100/mo to use TVE (30 fps / stereo sound) as the only way to view the content they paid for.