CI 3.1 for Website Building Platform

Keep in mind since Oracle bought MySQL they've not done much with it and in fact 5.7 was supposed to have many more features than it did. (I skimmed the news, so I have little details about it).

From what I've read, many (most?) hosting providers will be going to MariaDB, which is from the folks who originally built MySQL and accepts all the same commands. If all of this is true, MySQL support will drop significantly (it'll still be around for a long time though) from the hosting provider standpoint.

To your questions, there's different ways to do the database. You can create a database for each website or use the database prefix in a single database... What you'll need to worry about more than that, is if you get a few websites with serious traffic you'll be in trouble if the database can't keep up.

I agree with the advice above, you'll need to worry much more on the JS things. CI is pretty great for building ajax requests.