Shell DEP recommends Earth fault protection set point to be higher of 6A or 3% of the motor full load current. This seems reasonable.

Yep. Set ground protection to 5 - 10A and be done with it. If your system is high resistance grounded, you can have the chance to bring that ground fault protection down to 10A or below to mitigate the damage on motors due to ground fault.

Dear Mr. Emadshaaban1987 (Electrical)(OP)8 Aug 22 12:58
"...#1. How to select the earth fault protection set point for the low voltage electrical motors? #2. Does it depends on the system voltage, motor size? Earthling system type? ..... an example: 0.4kv 37kw induction motor, neutral is direct connected to ground?"
#0. To answer your question, I refer to IEC,BS,NEMA,NEC ; sorry NO [good/definitive ] advice from the mentioned publications/standards.
#1. I am of the opinion that the following should be taken into consideration:
a) say (1.5 x the leakage current) of a [health] motor. See also f) below.
b) not exceeding say [0.03 x motor rated current].
c) fire fighting pump motor may be set in the same way but only (alarm) [no tripping ! is allowed ]
e) essential loads may set 0.1 x higher or [only alarm without tripping].
f) for EF protection, (one zero-sequence CT) is preferred, instead of the residual/summation of three CT method.
#2. Yes. See #1. above.
Che Kuan Yau (Singapore)