When batch publishing models, you have the option to use Revit's visibility settings for the current view you have open in Revit.
The Assemble Add-in will honor Category and Workset visibility settings in Revit when publishing to Assemble. Worksets that are turned off for a particular view will not be published to Assemble, when opting to Filter using current view's visibility/graphics overrides.
To use the Visibility/Graphics option, select the check box next to Filter using current view's visibility/graphics overrides.
For an example, if furniture is filtered out of the current Revit view you are in, and you select the option to filter using current overrides, furniture will not be published to Assemble.
Be sure you are aware of not only the host model settings, but also of the linked model settings.
By leaving the check box unchecked, all publishable objects in Revit will appear in your Assemble database.