It took me a while to figure out why most apps still make sounds when the device is muted, but I think I get the paradigm now, or at least this is how it seems to work in practice:
'Mute' is to silence 'push' sounds (ie. email, text messages, phone calls) and the keyboard. The volume control can silence apps (ie. turn down the volume if you don't want to hear an app).
Would it be possible to make Skritter just work off the volume control, and independent of the mute switch? That seems to be what many iOS apps do. I almost always have my iPad muted, and the only app Icurrently have to unmute it for is Skritter.