[KevinH]

Lack of a unique book id can cause some ebook organizing software to slow down because the book's unique id is often used alone or in combination with the modification date and time to uniquely identify a specific instance of the epub.

Also duplicate ids in an opf depending on where it is used in the opf can result in broken metadata or missing spine items, or lost manifest data.

You should probably fix those issues, little by little. Use the calibre editor to fix those issues or something like Sigil.

If you understand the form and function of an epub OPF you could fix things in the opf using simple text editor.

A batch script to add in the bookid metadata would be doable but if epub2, do not forget to update the unique identifier used in the ncx as well.