It still doesn't sound right to me.

Unless the shares were bearer shares (which I know are more common in the USA than here) all the certificates were was paper. The true ownership of shares (perhaps subject to trust obligations or claims but that is another story) is (in the UK) determined by the state of the register kept by the company. The shares (the bundle of rights comprised in share ownership) would not have become bona vacantia simply for lack of evidence of an owner. If there was a will then they vested in the executor ex officio. If not then in the UK technically they would have vested in the Public Trustee (precisely to stop them becoming bona vacantia) pending the appointment of an administrator.

Once I got a grant de bonis non adminstratis in respect of rights that had lain unadministered in an estate since 1911. There was no suggestion that the rights had become bona vacantia. It was only one wrinkle of a film rights case that was the first one in which I had to deal substantially with pre-1911 UK copyright law...