It is fairly common knowledge now that the Australian Embassy in Bangkok do not print sticky visas anymore that are placed in your Thai partners passport they now only do what is called label free visas which now is a piece of A4 paper with all your Thai partners details on and a unique reference number.
The benefits of this are if your Thai partner lost their passport then they could be issued with a new visa immediately once they had got their new passport and also if the visa was lost it could be replaced with an e-mail from the Australian Embassy Bangkok.
Label free visas are also used for Australian settlement visas and also Fiancee visa application or known as prospective marriage visas and when you submit the visa application now the passport is returned to the applicant so their is no chance of a lost passport and when your documents are returned for collection to the Australian VFS in Bangkok the label free visa is in the package with your documents.
So please do not be alarmed if your passport is given back or the passport does not have a sticky visa inside it is common practice now and a very impressive system.