No they will be controlled just fine, The 4th pin is for PWM.
PWM (Pulse width modulation) Is the ability to adjust the rotation speed on the fly without changing the input voltage delivered to the cooling fan.
Your motherboard will be able to control them with voltage.
You can control a 3-pin fan connected to your mobo - be it on a 4-pin or 3-pin connector - via software like Speedfan. etc. Fans connected to the mobo are usually controlled by bios, but can be overridden by software. Take your cpu for instance with a 3-pin fan connected. Your bios has a listing of thermal limits (Tcase) for all CPU's that is supports, so when it detects your cpu the bios might be setup for instance so if CPU temp > 75% of Tcase set fan to 12v (or 100%); if CPU temp < 50% it might just send 5v. for 3-pin connectors the rpm reading is meaningless to the system itself, it's just an output signal for the user to interpret.
With PWM 4-pin fans however it's a different case. The fan is pulsed with 12v or nothing at all, and those pulses go for a set length of time, a width if you may... hence the name pulse-width modulation. PWM is more efficient as the fan is not constantly receiving voltage. both 3-pin and PWM fans adjust speed according to the same table of temps, just the control of speed is handled differently.