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The serialization format for the notifications is hard-coded in the platform : the class org.eclipse.om2m.commons.constants.Constants has a NOTIFICATION_MMT attribute defining the notification format to XML, regardless of the Accept header of the subscription query.
A possible fix (that solves my use case) is to use the request primitive content type to determine wheter to return xml or json content. However, this behaviour prevents from returning xml to a json request and vice-versa.