You can embed U3D as discussed in the following article (https://groups.google.com/d/msg/pdfnet-sdk/7lB27MPpKhQ/sP8PLszuKJ0J). U3D files can only be used in form of 3D annotations (sect 13.6.2 in ISO32000).
According to the spec, any annotation can be added to specific OCMD via OC entry in annotation dictionary. Before the annotation is drawn, its visibility is determined based on this entry as well as the annotation flags specified in the F entry. If it is determined to be invisible, the annotation should be skipped, as if it were not in the document.
I am not sure if Acrobat respects this key though. If you find any sample PDF that behaves as you would expect (e.g. in Acrobat) you can use CosEdit (http://www.pdftron.com/pdfcosedit/downloads.html) to inspect the structure of the annotation and OCMD dictionary and recreate the same structure in your code.