Make sure your headinclude_bottom template correctly includes {vb:cssfile additional.css}
headinclude_bottom is correctly included by the main template for wiki pages, so it should be included on wiki pages.
It is possible that whatever custom CSS you have defined in additional.css is loaded and working, but simply is not applying to elements on wiki pages. Wiki pages use different CSS classes than the rest of the forum. This is intended to give you more flexibility, so you can make the wiki look a little different if you want to.
But it might have nothing to do with additional.css and might be your style variables being deleted. This was a known vBulletin bug, and I thought the current Lite release implemented a workaround (see:
https://www.vaultwiki.org/issues/2857/#note14921 for details). As discussed there, you can restore your styles while VaultWiki is still installed, by running the vBulletin upgrade script even though there is nothing to upgrade.