Significant differences between Cookies and JWT for native mobile apps

I cannot speak for Android but on iOS cookies work with URLSession as good as headers. Once you can utilize the (standard) API right (e.g. dedicated, properly configured session with cookie storage per web app...), iOS should be a rather negligible factor to this decision.

_{We software developers (sometimes) have the tendency to apply the new hot thing everywhere we look; it's possibly a variation of the saying if all we have is an hammer, everything looks like a nail where in this case we just feel a desperate urge to use this new thing we learned about.}

One interesting point about this comparison is that neither JWT or Cookies are in fact authentication mechanisms on their own; the first just defines a token format and the second is an HTTP state management mechanism. Only this is sufficient to give us an indication that advocating that one is better than the other is wrong.

It's true however that both are vastly used in authentication systems.

Traditional server-side web application have used cookies to keep track of an authenticated user so that they were not forced to provide their credentials at every request. Normally, the content of the cookie would be an (hopefully) random generated unique identifier that the server would use to find session data stored on the server.

However, for a new type of web application - the API - it's more much more common to accept a token (in JWT format most of the times) as a way for the server to decide if it should grant access to who's making the request. The reason for this is possibly because while a traditional web application had one major type of client, the web browser, which has full support for cookies, the API's are generally used by much simpler HTTP clients that don't natively support cookies.

I think this is also why we could possibly argue that token based authentication makes more sense for native mobile applications. These applications generally depend on a server-side Web API and we've seen that if the API supports tokens it will increase the range of clients that can use it, so it's just the most practical thing to do.

In conclusion and to try to answer your concrete question, I would say JWT's do have an advantage over cookies on native mobile applications just because of the fact they are currently in very common use, this means more learning resources, SDK's, known pitfalls (mostly because someone else already did it and failed), etc.

Nonetheless, only use them if they give you the security assurances you need and end up simplifying your scenario. If you haven't gone through it already, I think you'll also appreciate Cookies vs Tokens: The Definitive Guide.