Well, first off, being a larger operation certainly doesn't prevent shutdown. Although it may add some peace of mind, there's a risk in trusting any third-party service provider.
Secondly, you can easily make use of the API to backup your bookmarks [1]. A simple cronjob can make a daily repo of everything, just in case.
I've been using Pinboard for about two years now, and I love it. It's simple, easy to use, and does what I want--and nothing more.