root in both public_html as private_html

My site runs on http (public_html) and a mirror runs on https (private_html). Could this cause issues with the vbSEO installation? Are there any settings that I need to consider?

vBSEO will only run on 1 url. It will use the vboptions -> site url setting to make all links. So, whatever setting is there, after page 1, it doesn't matter as the entire site will go to that url.

Do I understand it correctly that I cant use vbSEO due to my dual root directory setup?

You can use it, you just need to chose one or the other, or use htaccess to control your secure pages, and not have a duplicate file system

I use the https directory for subscribers and the http dir for all other users. Both directories are exact duplicates.
I understand that I can only enable vbSEO for one of these directories, which would result in inconsistencies between the directories. I will review if this causes serious issues not.