index: use has_node instead of ls

Current code doesn't work for prefixes longer than one, which makes index cache
effectively not work and it should've used has_node from the very start anyway.

pyproject.toml

@@ -35,7 +35,7 @@ dependencies = [
     "configobj>=5.0.6",
     "distro>=1.3",
     "dpath<3,>=2.0.2",
-    "dvc-data>=0.41.0,<0.42",
+    "dvc-data>=0.41.1,<0.42",
     "dvc-http",
     "dvc-render>=0.1.2",
     "dvc-studio-client>=0.1.1",