Enable Ruff rule family "N" and "S"

[DanielYang59]

Summary

Follow up #3871:

• Enable Ruff rule family "N", fix violation of NPY002 (the use of legacy np.random)

NumPy recommends using a dedicated Generator instance rather than the random variate generation methods exposed directly on the random module, as the new Generator is both faster and has better statistical properties.

• Enable Ruff rule family "S", for security related checks.
• Fix DTZ003 (deprecated datetime API).