Ok, I tried it, and as I assumed it had no effect apart from stopping SMPlayer playing through ALSA at all. I'm guessing this is a glitch in SMPlayer, because MuseScore plays fine through ALSA and makes the ALSA-Jack client appear. This solution still seems functionally identical to my ALSA loopback setup - most things work fine but Firefox still creates a "Firefox" Jack client and outputs through that instead of the default ALSA device.
Also, this deviates from the point I was trying to make in the first email - Jack's system ports can't currently be hidden from programs, and it would be useful if they could.