According to the official Microsoft Notification Area Guidelines[1], the notifications area icons have several usage patterns.
From all those, I think that only two apply to Ubuntu One:
When Ubuntu One is idle and starts syncing/has a notification to show it should behave as a "Temporary Notification Source": the icon only appears to hold on a notification. According to MS:
"Temporary notification source
Displayed temporarily to show a notification. Removed after a timeout, or when the underlying problem is addressed or task performed. "
Temporary icons are preferred for pure notification sources. Don't display an icon that doesn't provide useful, relevant, dynamic status just because a feature might need to display a notification in the future. "
When the notification fades away, U1 notification area should behave as a "Temporary Event Status"(as U1 has desktop presence): the icon is shown to indicate progress. According to MS:
"Temporary event status
Programs with desktop presence can display icons temporarily to show important events or changes in status.
In this example, icons for printing and installing updates are displayed temporarily to show important events or changes in status."
This is not what happens at the moment, as the Ubuntu One icon is always shown, even if hidden by the windows notification area protocol.
[1] http://msdn.microsoft.com/en-us/library/aa511448.aspx
If 2 of them apply I would assume then that the use of a notification icon is correct, right? Also, the U1 application does not have desktop presence, that is, it does not have a windows opened. I'd prefer focus on the bug you already reported lp:681869