Usually nodes aren't created while the simulation is running. It's not forbidden (what's forbidden is to destroy them), but for sure it's... unusual.
What can be a bit wobbly in creating the nodes at run-time is in the initialization phase of each layer. Still, even if it's not theoretically illegal, for sure it's something we don't test. Hence, I can't exclude that there aren't code issues when you try to do it.
Instantiating the nodes before Run is for sure the best option. If you need them to be completely "silent", just move them to the Far Far Away Kingdom (usually 2Km apart from any other node does the trick). When it's their time to "show up" just move them where they should be.