Will the MachineLink still monitor my utilisation if my machine is down under maintenance?

Yes.

If your machine is going to be off for a long period of time and you don't wish the time to be recorded as downtime, you can switch off the MachineLink for that machine.  
If the MachineLink is switched off at the mains, the timeline will show up as the machine is 'Offline'. If you don't switch the MachineLink off, the MachineLink will assume this is 'Downtime'.
Once the machine has been fixed, please do remember to switch the MachineLinks back online at the sockets.
If you have any questions contact Customer Success at support@fourjaw.com