It may work but you better connect all vcc/avcc pins to power source. I had a problem without giving avcc(44) power when programming flash(I can't remember it was ISP or USB bootloader), IIRC.
Asumming the mcu is ATMega32u4 note that pin 44 is actually AVCC, not VCC and I think it is not connected internally, also pin 2 is UVCC. Not ciritical for you design in fact, though, you may want to check datasheet for next interation.
When any ratsnest lines are drawn in the CAD as your pic shows it means that you don't finish routing tracks yet. And DRC must be always your good friend, you would receive waring for the unconnected pads from it in this case.