So I'm looking at getting a Magni and Modi by shiit and it connects via a USB cable, I was just wondering if I extend the cable so I can sit the device on the other side of my desk will it affect the sound?

nope its digital it either works or it doesn't and unless your desk it 30 feet long it wont be an issue

Fantastic, Thanks for the reply.

Will using a cheap ($3.80) USB A to USB B cable (3 meters) make some impact on quality, or do I have to spend $100 on some magic cable?

Nope a digital cable either sends the electrons or it doesn't, don't let anyone convince you otherwise... no magic cable will make a difference. Although in some situations when using a USB powered device you have to be careful about cable length, since the resistance of the wire will over long lengths reduce current. But this is only in extreme situations, mind you.
 
Edit: A magnetically shielded cable may make a difference depending on electrical interference, if that can be considered a "magic cable."