How to delete element "bpmn:Message" using modeling?

Sorry for misunderstanding.
For getting underlying Message element you could do something like this:

var is = require('bpmn-js/lib/util/ModelUtil').is;
var getBusinessObject = require('bpmn-js/lib/util/ModelUtil').getBusinessObject;

var messages = modeler.get('elementRegistry').filter(function(element) {
  var businessObject = getBusinessObject(element);
  var eventDefinition = businessObject.eventDefinitions && businessObject.eventDefinitions[0];

  return is(element, 'bpmn:BoundaryEvent') &&
      !element.labelTarget &&
      eventDefinition.$type === 'bpmn:MessageEventDefinition';
});

messages = messages.map(function(m) {
  return getBusinessObject(m).eventDefinitions[0].messageRef;
});

console.log(messages);

Cheers,
Vladimir