Most motherboards are good for about 1 amp of fans(remember fans have a higher peek power that has to be taken into consideration).
If the board can control with voltage(You have to watch this as some boards just run 3 pin fans full speed all the time even on 3 pin headers) then yes they would both be controlled with a splitter. It is best to contact Asus to see the current limit on the fan header of the board.
PWM fans have the advantage of not requiring a regulator to lower the voltage for speed(they always get 12 and the fan controls speed with a pulsing duty cycle signal) reduction and should overall be cheaper to implement on the board.
I have personally run multiple low speed fans off of a single board header without issues, but every board and fan combination is different.
If you do use a Y cable, You would check if it has 2 speed sense(yellow most of the time, it is the third wire) wires and remove one to avoid speed misreads. I have no clue why they even make them this way to begin with(Noctua's included 3 pin splitter was built the right way).