Did you miss that Sweden, USA and the UK intelligence agencies were helping Estonia establish its own after having kicked out the KGB?
The fact Sweden seemed to have known about the accident as soon as it happens implies their intelligence was tracking the vessel. The UK suddenly becoming a Baltic nation and signing the Treaty forbidding anyone to visit the site, together with ignoring an act of parliament that ensures UK citizens have a right under the Freedom of Information Ac to inspect public documents, should tell you all you need to know.
As the accident was never properly investigated then all we have is speculation. Given Sweden admitted to smuggling out FSU state secrets on the Estonia passenger ferry and it took a whistleblower to come forward, likewise for that of the two cargo planes from Arlanda, it is clear the whole episode has been labelled 'classified' and all the public gets is a soporific story based on the Herald of Free Enterprise.