However, NodeBodyUpdate object in updateNodeCall method doesn't have a secondaryChildren field.
One approach I considered is to update secondary children with additions (createSecondaryChildAssocationCall) and deletions (deleteSecondaryChildAssocationCall) resulting in an overhead due to several REST calls.
Ah, the typical consistency problems when a new ReST API is being developed. I would advice you to look for or create a new JIRA ticket to address the lack of secondary child association handling in the node update request body. At the moment, the createSecondaryChildAssociationCall you already mentioned would be the only way to go until the API is expanded. Richard Esplin has on multiple occasions mentioned to me that there would be some kind of "batching" feature in the future of the ReST API, but I neither know if that would allow to execute two operations in one HTTP call nor what the status is on that...