I'm using a variant of Vancouver and my documents are not published, as such. I'm a medical writer and they're used in a variety of end products, from editorials in magazines to printed materials like brochures. I remember seeing a checkbox when I started my last document but I can't see that anywhere now that the document is in progress.
The only checkbox related to journal abbreviation in Vancouver is in the document preferences > Advanced Options > Use MEDLINE journal abbreviations. And it will only work if you don't have "Journal Abbr" field populated in your items.
Which style are you using/where do you want to publish your document?
I remember seeing a checkbox when I started my last document but I can't see that anywhere now that the document is in progress.