I am buying Booking Calendar paid version. Do I need to make future updates from WordPress directory?

No, you do not need to make update from WordPress directory, because then you will use Booking Calendar Free version.
We will send to you update(s) of your Booking Calendar version (if these update(s) are ready) by email directly, after you are request update at this page.
You can check according new updates at this page.
Please check about ability of getting free updates here and here (if you was purchasing your version from 15/12/2013 until 15/12/2014).