Just as a heads up; Jigsaw (as it is today) doesn't have versions, so the issues you describe won't happen. There will be one global json-lib module that will be available to all modules.
They've taken enough to get to this point that adding version numbering isn't going to happen, but it doesn't rule it out adding it in the future. They did the minimum necessary to split out the Java libraries into different modules but no more.
If you want to have versioned dependencies, you have to work with a module system that understands versions, like OSGi.