You are confused. "What's growing here?" does not mean "What is it growing here?" The meaning is рости, whether it's present simple or present continuous. There is no complication.
For example, on seeing a group of plants, one might say "What's growing here?" or "What is this (that's) growing here". On wondering what might grow in a particular place, one might say "What grows here?", although it might be more natural to say "What can grow here?" or "What kind of plants grow here?".