That is a holdover from previous expansions and totally unnecessary for Horde players now. Alliance still has a higher win% but its comparable to the higher win% HOrde has in all the others.
The IoC one always confused me. Alliance has kept the same strategy of going docks in mass and conceding hangar, but all it takes to counter this strategy is a few Horde players willilng to sacrifice themselves to kill the first wave of glaives. Do that and the Alliance strat dies and Horde wins easily if the majority go hangar and run bombs.
http://wow-stats.com/bgwr01.html