Perhaps, but you wouldn't actually want to run a Scala program that way.
To implement C semantics, Emscripten uses a single, large JavaScript typed array as the heap. To the JS garbage collector, this heap is a big, opaque blob. Then your Scala Native program has its own garbage collector operating within its heap. The two garbage collectors are unaware of each other. This is just a vague intuition on my part, but it seems to me that an arrangement involving nested garbage-collected heaps is bound to be suboptimal. Scala.js is much better in this regard, since Scala objects are just JS objects, sharing a garbage-collected, compactable heap with the other JS objects.
To implement C semantics, Emscripten uses a single, large JavaScript typed array as the heap. To the JS garbage collector, this heap is a big, opaque blob. Then your Scala Native program has its own garbage collector operating within its heap. The two garbage collectors are unaware of each other. This is just a vague intuition on my part, but it seems to me that an arrangement involving nested garbage-collected heaps is bound to be suboptimal. Scala.js is much better in this regard, since Scala objects are just JS objects, sharing a garbage-collected, compactable heap with the other JS objects.