Actually it wasn't going away but greyed out, when none of the vaults was unlocked.

I can confirm this issue since the change from AWT to libappindicator on Linux.

This can be fixed here: https://github.com/cryptomator/integrations-linux/blob/7b725185805d74e993cd73d2089325269c726a75/src/main/java/org/cryptomator/linux/tray/AppindicatorTrayMenuController.java#L96-L106

switch (item) {
	case ActionItem a -> {
		var gtkMenuItem = Gtk.newMenuItem();
		Gtk.menuItemSetLabel(gtkMenuItem, a.title());
		GObject.signalConnectObject(gtkMenuItem,
				"activate",
				GCallback.allocate(new ActionItemCallback(a), ARENA),
				menu,
				0);
		Gtk.menuShellAppend(menu, gtkMenuItem);
	}

by adding:

switch (item) {
	case ActionItem a -> {
		var gtkMenuItem = Gtk.newMenuItem();
		Gtk.menuItemSetLabel(gtkMenuItem, a.title());
		GObject.signalConnectObject(gtkMenuItem,
				"activate",
				GCallback.allocate(new ActionItemCallback(a), ARENA),
				menu,
				0);
		if (a.enabled()) {
			gtk_widget_set_sensitive(gtkMenuItem, 1);
		} else {
			gtk_widget_set_sensitive(gtkMenuItem, 0);
		}
		Gtk.menuShellAppend(menu, gtkMenuItem);
	}

which is already available in <artifactId>libayatana-appindicator-java-full</artifactId>, but not yet in <artifactId>libappindicator-gtk3-java-minimal</artifactId>.

I'll add it there as a nice function, taking a boolean as the second parameter instead of an int, release a new version of the bindings and provide a code update for Cryptomator.

@purejava any reason the fix is not merged into the code itself?

Yes. Cryptomator uses the minimal flavor of the appindicator library, which has a smaller file size and results in a smaller Cryptomator package on Linux.

I need to re-generate the minimal flavor of the Java bindings with an added gtk_widget_set_sensitive function.

Requires a new release of https://github.com/cryptomator/integrations-linux

Fixed with commit fb4f9fc