The ArcPy GetCount function returns the number of features in the feature layer with a definition query applied instead of the number of features in the feature class after using the ConvertLabelsToAnnotation function if the feature layer and the feature class have the same name.
Get Count runs against the actual feature classes on disk. Converts Labels to Annotation runs against the layers in the map. Its outputs, _anno feature classes, include the layer definition. Get Count does not honor layer properties--that's why the _anno feature classes are not counted.