Choose and protect NPN transistor with resistor and diode
Your diagram lacks grounds but I can get the idea.
It would be better to switch the 9V with the transistors. The current will be lower and the step-up module may have some nasty characteristics (like a big input capacitor) that could cause problems when it switches on. The DC current switching the 5V might be in the 75mA range vs 35mA switching the fan directly.
The purpose of the resistor is not just to prevent the transistor from dying but to control the base current so that it saturates when on. The 1K may be a bit too high for that purpose. BC547B is okay with Ic/Ib = 20.
With 3.1V drive and 0.7 Vbe the base current is 2.4V/R. So for 75mA you'd want about 620 ohms and for 35mA 1K or 1.3K is okay.
As far as the diodes go, I am not sure they are actually necessary, even with the transistor switching the fan directly, but it costs little to add them. Any of the types mentioned are fine. I would use 1N4148s or 1N400x.



simulate this circuit &ndash; Schematic created using CircuitLab
The only disadvantage of leaving the DC-DC converter(s) running all the time is a bit more power consumption from the quiescent current the step-up converters draw, but it should not be much in comparison to the ~1W the fans draw in operation.