Actually for this I was referring to the front-end usage, not the back-end tree.
For all of the resources created by Articles, by default, hidemenu is set to 0. Articles hides the hidemenu checkbox, so I thought if I could get the checkbox back and tick it then the items would show in the front-end menus.
In the end I did a bit of a hack, I went into two files, the first was /assets/components/articles/js/article/create.js on line 266 and the second was /assets/components/articles/js/article/update.js on line 454 and added this:
{
xtype: 'xcheckbox'
,name: 'hidemenu'
,fieldLabel:_('resource_hide_from_menus')
,value: 0
,checked:false
,id: 'modx-resource-hidemenu'
,value: config.record.hidemenu
}
Then the Hide in Menu checkbox appears on the resource, which I can then tick to make the items appear in the front-end menus. Its very hacky, and next time I update the Articles component I'll loose my changes, but it works for now.