You are correct, Notes dont seem to go anywhere on the Zaurus.
I made a new task with Qtopia desktop, Gave it a name and put some notes in it.
Synced the task and it showed up on the Zaurus sans notes.
Changed the name of the task and synced it back to Qtopia Desktop and it showed up with its notes in task.
In a strange occurance I have a task that has a different Name than Description on the Zaurus side, on the PC side I only see the Description and not the name!