Can I log employees' working hours through Bonjour availability?

It looks like you want something like NetSpy or ActyMac to monitor employee activity. It will handle what you want and more, although I'm not sure I would suggest the orwelian approach to employee management.

You may want to look into a pure network monitoring tool like Paessler.

The easiest solution would be for you to just monitor the server log on your OS X server for the time the user logs-in and logs out. A simple script that tracks the time and totals them into a spreadsheet using a nightly cron job.

You can also just use the last command as seen in the screenshot aslong as the file has not be cleared.

You may want to try other basic unix system logging scripts.