Yes, this can negatively affect SEO, because vbulletin does not allow you to set a language for sub-forums. Therefore SE will index forums that are in other languages as the main language set in admincp.
So your English forums will have a lang="ar" instead of lang="en" and are therefore set as Arabic forums.
I am not sure if SE would still classify non-Arabic signs as Arabic, but if not, then SE will not know what language your website is in.
You need a hack to be written to resolve this. You can post a paid modification or a free modification request in the appropriate forum.
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