How are the two 6 cell packs wired? Series, parallel of one for each motor?
If in series, using a 3S pack will reduce voltage and thus performance. If in parallel, the increase in voltage might lead to issues with the controller, as well as a possible shortening of motor life. Performance would increase, but so would current consumption. Run time would depend on how much more capacity the 3S has.
If the ESC instructions say Max volts 8,4, then any more is not advisable, even at part throttle. PWM ESCs are either switched fully on or fully off - the circuits that drive the output transistors tend to be the limiting factor, and will overheat, usually cooking whatever is near them.