JUnit testing for reading JSON files

As per maven's standard directory layout, I would advise you to put you JSON test files in src/test/resources since they are test resources. Note that you can (and should) organize your own folders hierarchy under the resources folder (other developers would find it easier to locate specific test resources when fixing or adding some other tests).

So yes you would end up with your JSON files somewhere but not anywhere if your own test resources hierarchy is good enough (for example, if you think your package structure is well organized with meaningful package names, following it for your test resources hierarchy isn't a bad idea at all).

You should ask yourself what the mission critical code is for your project - reading files or parsing their content. For my projects, parsing was the interesting part, so I placed files to parse as test resources, read them in the unit test to string and pass them to the parser to unit test the parser. It is also possible to include the contents directly in unit tests as big ugly strings, but when you have a dedicated place for test resources, why not use it.

Copypaste the contents of the example file as a String variable in the test code

I suggest against doing this as it makes modifying the input for your tests more difficult. Also, using an external file makes your tests more flexible. For example, reading an external file allows you to create multiple tests while reusing the basic framework for each test. Of course, this also means that you will need to take some time to design the methods that actually perform the tests.