Now, when it comes to how fast a motor spins (which determines how fast your car goes!) - then the volts comes into play. kV ratings on a motor tell you how many RPMs per volt you will get at full power. at 7.4V, as 3500kv motor will rotate at 25900 RPMs, and 11.V will rotate it at 38850 RPMS - hence a 3S 5000 will definitely go faster than a 2S 8000 battery.
Motors are rated for a certain wattage - let's say the VXL is rated for about 600 watts (it might be higher or lower - let's just estimate here!)
So, at 7.4V - it will pull 600/7.4 = 81 amps
and at 11.1V-it will pull 600/11.1 = 54 amps (yes, lower amps!)
When a battery is placed under load, the voltage drops. The closer the load approaches it's max, the lower the voltage dips, and the hotter the battery will get. So, since a 20C 5000mah battery will be approaching it theoretical max of 100amps (81 amps out of 100 available), the voltage will dip more than it would with the 20C 8000mah battery (81 amps out of 160 available). So, even though the 2S batteries are both rated at 7.4V, the 8000mah will be faster than the 5000mah.