If you check at GList, it hasn't a GDestroyNotify at initialization, like GHashTable, no g_list_remove() returns data to handle by Vala automatically, then is your responsability as a programmer to know how to handle data, in this case each time you call GLib.List.remove() on ref counted objects, you should decrease it by calling unref() explicitly in Object classes or the one provided by your bindings.
So if GLib adds a new GLib.List<Object>() specialized handler for GObject classes, taking care about ref/unref, we just take care on using GLib.List<G> on Objects and use Gee.ArrayList<G> instead.
Use GLib.List<G> as returning value where your class takes care about your objects not returned GLib.List<G> one.
If you create a GLib.List<G> as return value, creating one using append(), as described, advice your user to unref() all returned objects using GLib.List<G>.foreach() before get out of context.
For public API you may want to use GLib.Queue() instead, it returns removed objects, then it can be unref() by Vala automatically.