Very good question… there is always going to be a risk whenever someone updates WordPress, a theme, or even a plugin. I always recommend “everyone” to have a method of backing up their site and site files before they do any kind of update, especially with WordPress. There’s a few plugins out there that does backups, but you may want to consider VaultPress.
How future updates of WordPress will affect your third party plugins, or even other themes will always have a risk, but for the most part, you should be ok. It also depends on what version you are upgrading from as well, so if you’ve been on 3.6.0, then going to 3.6.1 should be fine. But, I still say always keep regular backups.