@kerner The hidden shapes in your document are marked with docPr.hidden attribute:
<wp:docPr id="66" name="LogoSW2" hidden="1"/>
I am afraid, currently there is no public API in Aspose.Words to access this property.
We have opened the following new ticket(s) in our internal issue tracking system and will deliver their fixes according to the terms mentioned in Free Support Policies.
Issue ID(s): WORDSNET-26193
You can obtain Paid Support Services if you need support on a priority basis, along with the direct access to our Paid Support management team.