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My answer has very little to do with either technology specifically. If you want to avoid data integration headaches, you have to be consistent, meaning that every developer has to do things in a similar way, rather than defining their own set of data representations. To do this requires a process that is:
A) very easy for developers to use
and
B) very quickly gives developers consistent representations
A simple example: if developer A and developer B both need to share information about user accounts, and one uses a variable length text field and one uses a fixed-length numeric field, you have created needless inconsistency, through the lack of a clearly defined process.
Taking this one step further, if your clearly defined process has future flexibility baked in, for example by making it possible for some future program to process today's N-digit account codes as well as tomorrow's N+M-digit account codes, you can carry that flexibility along into the specific implementation.
Also, bear in mind that JSON is implemented as JavaScript, and is therefore subject to all of the strengths and vulnerabilities, particularly from a security standpoint, as other uses of JavaScript.
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