After whipping up a quick script to kill and restart jackd when my laptop goes into S3 (/etc/pm/sleep.d) I had a revelation: any processes connected to jackd would have to reconnect. This doesn’t happen and sound is just lost. So for jackd to be usable on a laptop they need to support S3 directly and currently in the Debian unstable repositories Jackd doesn’t.
I gave esound a try in place of jack but with totem esd ran the cpu up to 20% for a flash movie which is pretty nuts. It had a noticeable impact on the video playback so esound got uninstalled as quickly as it was installed.
Finally I just fell back to using alsa directly. This actually worked perfectly and I’m not sure why I didn’t just go this route in the first place.