It is not missing. Almost all functions/features of productivity tools are directly integrated into S Note in Note 3.
The only noticeable exception is Wolfram formula search, which is integrated into S Finder.
To use all other features in productivity tools, you can simply write or draw first, then select them to convert (to shape, formula, or text). To select, you can tap the select button, then draw lines around the parts to be converted.
