Is there something like japicmp for kotlin MPP ? Obsiously it will not be able to work on binaries but maybe at the source level ? Or using metadata ?

No. We (Android) use UAST to parse signatures and emit signature files in a tool called Metalava. The tool should work fine on native and JS sources, but we haven't tried it yet.

I just bumped into this: https://github.com/Kotlin/binary-compatibility-validator. Not really sure how it works yet but that sounded promising.

It's JVM-only and uses Java bytecode signatures