What is benefit of diode in the RC circuit
It looks non-functional doesn't it!

However, the designer has cleverly anticipated what happens when you cycle the power on this circuit. When the 5V goes away, without that diode the capacitor would remain charged for some time. Reapplying power too soon might prevent the reset signal being generated.

The diode provides a short path to discharge the capacitor when the rail goes to ground.

It may however be superfluous if the input of the device has internal diodes to protect it from over-voltages on the pins. But even then, those diodes might not like 10uF charged to Vcc over Vcc hung on them.

BTW it is a common mistake to forget to think about, and designing for, what happens when the power is removed. 

Your second question... See Transistors answer. Generally devices like this indicate how the crystal should be wired in their data sheet. It is important to accurately follow their recommendations. Even then, once the PCB stage is reached, some tweaking can be required.