Wordpress - What is the problem if I use CDN in my WordPress parent theme(built using bootstrap)?

Your theme should not depends on any external link library. There is no guarantee when that library can be taken down. That's the reason all of your theme assets should be package with theme, to prevent the future risk.

As daniyalahmad said, it is better not to include links to external assets in your theme. A good example of this recently. I use a theme from MyThemeShop and they linked to external html5shim. Google just recently stopped hosting this and so I started to get a 404 on my website. It was easy for me to simply comment it out, but for typical users, this is a big problem.

There are now 1.5M instances of a dead html5shim googlecode URL on GitHub: https://www.reddit.com/r/programming/comments/4u47ak/15m_instances_of_a_dead_html5shim_googlecode_url/

When packaging a theme, always package it with it. And if you don't want to include it, write a tutorial for your users on how to deploy it after the fact. If they want to link externally that is usually fine, but not in the base theme.