You are using IModelDoc2::SaveAs3 Method which is obsolete. Try using IModelDocExtension::SaveAs Method. With this method you can control Format in which to save the document, save as options and export data. See if you have the same problem.
I also tried IModelDocExtension::SaveAs Method, however it also doesn't work.
When you manually save an IFC, there is a message saying "One or more components are hidden or suppressed. Do you want to resolve them?".
I think it is this message / option I need to access through the API to say "No".
Unfortunately the Export data is only the PDF data, and the SaveAsOptions do not have any options for ignoring suppressed components..
You can still use this method because it's the latest I could find. For the parameters use Path, swSaveAsCurrentVersion, swSaveAsOptions_Silent, Nothing, ErrorOut, WarningsOut.
Use swSaveAsOptions_Silent, so all notifications from SolidWorks will be suppressed.
For Export Data just use Nothing (VB.Net/VBA) or Null (C#)
I've seen this issue. What I did as a workaround is exported to parasolid and then exported the parasolid to IFC.
I have found a way that seems to work very well.
Select and Delete all the suppressed components, then Export the IFC, then use swModel.EditUndo2().
This will then Un-Delete the components, returning the model back to its original state.
Hope that helps your guys too.