Unsafe usage of nlohmann::json::operator[]

Accessing a const object with the reference operator with a missing key is undefined behavior and yields a runtime assertion in nlohmann::json library.

The codebase should be checked for such usage of the reference operator. Fix is to either use checked access with the at() function or call the contains() function before referencing.

Usage of reference operator with non-const object is ok as any missing keys are added.