@Shadester posted a reply which for some reason doesn't show up when I come to the discussion. Here's what he said:
"Why would it be deliberate? It was there in Yosemite."
I have 2 answers.
The first is that if it was there in Yosemite, it could still be deliberate. In fact, that would be some evidence that it's been deliberate all along, in the sense that Apple doesn't regard that as anything that needs to exist in the OS.
But the second thing is that my recollection is quite strong that it did exist in Yosemite. So - undercutting my own conclusion stated above - Shadester's observation might point to this being another one of those OS glitches like the iCal glitch. The iCal glitch only occurs for some people. The glitch is that if you try to create a new event, when you finish and save the event, it reverts to "New Event." My wife has this glitch on her laptop running Mavericks, I did not have it in Yosemite, but now, in El Capitan, I have already had what I hope is an isolated event of it happening. Because while you can work around it, Apple has shown absolutely no interest in fixing it.
If that's the case, the only hope I can see to fix this Volume Control "glitch" is a reinstall, maybe even a clean reinstall. At which point you might trade one glitch for a different one.
My own solution is based on the fact that the headphones controls work. So I might connect my external speakers by dumping the USB connection & plugging the external device into the headphone port. Or maybe not, since I can just use the volume buttons on the external if I reposition it a little on my desk.
