Hello Jean,
i understand a bit more. I don't think that you can have a real full control over SEO if each subdomain are not running as independent installations of Joomla with different links, meta data, etc
I would focus on the main website using JSitemap to provide good sitemap, meta data and fix possible SEO issues.
If you want to talk with a SEO expert contact me at
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i can let you talk with my partner guy.
Cheers,
John
