1. Is this really the case, or can the USB and SleepTimer components work along on the same device (the "Clocks" configuration panel in PSoC Creator indeed allows to enable both the 1kHz and the 100kHz ILO clocks, see attached screenshot. What does that mean)?
1 kHz and 100 kHz clocks can run independently, are not synchronized to each other, and can be enabled or disabled together or independently.
2.Can the SleepTimer work on a 100kHz ILO timer clock? (obviously, that would shorten the sleep intervals by a factor of 100)
Sleeptimer can work only with the 1KHz ILO.
3. What other wakeup sources would be recommended to obtain long sleep intervals (in the order of 1 second) without considerably increasing the current consumption during sleep?
Do you need a periodic wake up?
Since the 1KHz ILO is enabled by default you will be able to use it for the SleepTimer. Are you facing any specific issues with Sleeptimer on the USB projects?