Your best bet wouldn't be to cover them with anything. Installing a a toggle switch would be extremely cheap and easy to do, and that way you'd be able to turn them off and on at your leisure.
You can really do that? Got a guide or link on it? I didnt think fans that had lights inside of them + leds didnt have the ability to do it unless designed so.
The lights in the fan's probably not. I clicked on the Newegg link to get a quick glance at the case and saw those two LED's in front of the fans, thought that's what you were talking about. Those could be done easy, as someone else said, LED's built into fans not so much most of the time...
Generally LEDs on the fan are hard wired to power on when the fan is running. You could either build a switch to turn off fan or unplug the fan to turn the lights out. You could also try a filter mask to cover the fan and still let the air flow.
There does appear to be buttons on the front of the first two pics...maybe go to a review site and see for sure, but looks like it.
Dont raise your temps man to 'compensate' for anything...its the CASE temperature for Pete's sake!
How are you going to do that and be more accurate than the software with a sensor precisely where it needs to be?
I mean, do it, but you are so worried about temps Im not sure I understand how this is going to help when its likely to be many times more inaccurate than the sensor...