There is FieldDefinition standard object, which is available in usual SOQL and in Tooling API. However, this object has different fields available in different ways of accessing it.
It has a field IsFlsEnabled which is only available in Tooling API, but it is possible to mitigate this problem by checking if IsNillable is true and if PublishedId is not System.
Field Level Security is not available for standard fields (which have PublisherId equal to System and LastModifiedDate null) and for required fields which are not Nillable.
So, basically speaking, IsFLSEnabled = IsNillable AND PublisherId != System and even though we can’t access IsFLSEnabled field in usual SOQL, we could calculate its value based on values of field IsNillable and PublisherId.
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