Electrical – Tachometer vs. Tachogenerator

They are probably meant to act as voltage clamps.

Presumably, J29 is a connector that is plugged into something in the outside world. A fan in this case. Transient voltage spikes could find their way onto the wires and travel into the circuit. If the transient voltage rises one diode-drop above B_VCC_AUX_5V, the diode will switch on and allow current to flow into the voltage source. The diode effectively clamps the voltage on the line to one diode drop above the voltage source, reducing the ability of the transient spike to damage any upstream components.

This circuit will probably get the job done, but is not necessarily the best choice of transient protection. Standard silicon diodes, such is as the 1N4148, have very low leakage currents, but are relatively slow to turn on. So transients may have time to damage circuit components before the 1N4148 clamps the voltage. TVS diodes are specifically designed to protect against transients in digital systems and would be well suited for this application.

It depends on how you are sensing the current. If you are just using a resistor to ground, then the photodiode will become forward biased and you get a maximum voltage of about 0.5V. (If you use a TIA opamp circuit that won't happen.) If you reverse bias it then you can get output voltages up to the bias supply. With a TIA opamp circuit the only advantage (as HH plasma said) is a higher frequency response.