The most likely reason for the missing data when viewing the 3D Web Scene in the CityEngine Web Viewer is due to the fact that the dataset was not symbolized with 3D symbology at time the .3ws file was created. Change the symbology to a '3D Simple Marker Symbol', in ArcScene prior to creating a .3ws, and then try to publish to ArcGIS Online.
3D symbology is only required for point and line features. Polygon features can use simple symbology.
The steps to symbolize a point dataset with 3D symbology are as follows:
1. Click the symbol in the Table of Contents.
2. Click Edit Symbol.
3. Select '3D Simple Marker Symbol' from the 'Type' dropdown menu.
4. Select 'Sphere' from the Style dropdown menu.
5. Click OK.
The 'Export To 3D Web Scene' geoprocessing tool can now be used to create a .3ws file and view it in the CityEngine Web Viewer.