С PDFBox:
PDDocument doc = PDDocument.load(...);
PDViewerPreferences vp = doc.getDocumentCatalog().getViewerPreferences();
if (vp == null)
{
vp = new PDViewerPreferences(new COSDictionary());
}
vp.setDisplayDocTitle(false);
doc.getDocumentCatalog().setViewerPreferences(vp);
doc.save(...);
doc.close();