Thanks for sending all this information to us. It is really helpful to find the issue.
It seems that the
init.d script is in an inconsistent state. In a regular reboot that should not have happened. In order to repair it, could you please execute the following command in your machine?
sudo sed -i "s/SERVICE_VERSION = 1/SERVICE_VERSION = 0/g" /opt/bitnami/nami/node_modules/provisioner/lib/recipes/system_services.js && sudo provisioner --only-recipes system-services callRecipes beforeInitialize
Then, reboot the machine to see if MongoDB starts automatically:
Reconnect to your machine, give some minutes to start and check the service status with the following command:
sudo service bitnami status
If the the service is running, you will probably need to do the same steps in the rest of nodes of your cluster.
Let us know if this solves the issue.