Almost all mobos today can support up to 1 amp load on EACH fan header. Most fans run under 0.2 amps, so 2 fans per port is surely acceptable unless they are REALLY high-power fans.
Ideally, a case ventilation fan ought to be controlled by a CHA_FAN or SYS_FAN header. Their automatic control systems are guided by a temperature sensor in the mobo. The CPU_FAN headers, on the other hand, are guided by the temperature inside the CPU chip itself.