Folders can be hidden by using the same mechanism that Alfresco uses. To hide a folder you have to add the sys:hidden aspect to it.
The sys:hidden aspect cannot be added to a folder from within Alfred Desktop. You have to do this by using the JavaScript Console of Alfresco. This is a code example to add the sys:hidden aspect (or any other aspect) to a folder:
var nodeRef = "workspace://SpacesStore/aad16fd3-74fa-45ea-9863-48b325359ccd"; // <-- Change this noderef, this is just an example
var nodeToHide = search.findNode("noderef");
nodeToHide.addAspect("sys:hidden");
nodeToHide.save();