As NtQuerySystemInformation is not encouraged to be used by Microsoft, I am looking for alternatives to display spectre and meltdown mitigation options set on the OS.

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As the documentation for NtQuerySystemInformation explains:

Applications should use the alternate functions listed in this topic.

Neither the SystemKernelVaShadowInformation entry, nor the SystemSpeculationControlInformation entry list alternate functions, so there is nothing you can do to avoid calling NtQuerySystemInformation while still using the functionality it offers.