Categories are stored as post meta. You can pretty much organize them how you want, but the meta table is flat, so you'd have to manage the organization yourself. Consider using taxonomy instead, it has a parent child structure that gives you much flexibility.
Consider storing custom post data with each user instead of the other way around. Just makes more sense to me. In the end, it probably doesn't matter, you use either post meta or user meta. No need for some special post hack to implement either way. You are limited on how to display data only by your ability to construct a mysql query to find and organize the data. You typically would use WP_Query objects to do this, but there's a generic db global access object called $wpdb for anything you can't do with WP_Query.
Out of the box, WP only has a public/private viewing structure. You can create any combination of user roles and capabilities to manage access. Custom view access is easiest done at the template level, but as a plugin, that's off limits. There's probably a number of approaches via filter and action hooks to manage access.
For example, you could filter 'the_content' just before it is sent to the client, and if the client has the wrong capability, you send an error message instead of the content.