Well the best thing to do is to check to ensure that the thermostat is working correctly. You can remove it and place it into a sauce pan and check to see if it correctly opens at the right temperature when left to boil.
If your daily commuting the bike, then leaving the thermostat in is advisable. Yamaha know what they're doing.
If you start tuning the bike and pushing it beyond its original specifications, then you may want to consider removing it.
The thermostat isn't just there to aid heating up of the engine, it also has a role in providing pressure in the cylinder head to avoid pocket stagnation of gases. So it's actually important it's fitted.
I just noted that these engines do run warm and removing the thermostat allowed my bike to run at a more consistent temperature when under load.

But still check those connections anyway to make sure they haven't vibrated themselves to pieces.


