Yes and no.
Typically, one install of XOOPS would run one website.
However, you could configure a single installation of XOOPS to have multiple groups of users in it, besides the standard Registered Users group. If two or more groups of users in the real world were all members of distinct groups in your XOOPS site, then you would be able to show them completely different content, but only after they had logged in to your site (until then, everyone sees whatever you have allowed Anonymous Users to see).
You could even hack your XOOPS so that depending on what group users were a member of, a different theme was used. I don't know exactly how to do that, I'm not sure if it has ever been done. But in theory I believe it is possible, since the user object, and it's group memberships, is determined before the template is applied to the page output.