It's a terrible problem. Maciej Ceglowski is doing his own study on link rot: https://blog.pinboard.in/2014/08/researching_link_rot/ He says my numbers match his own so far, about 5% per year. So I'd guess ~2200 bookmarks are dead, and maybe you could get ~1000 of them back from the Wayback Machine.

I have 28MB of personal bookmark files I'll be post-processing, as well as ~47,000 links from a shared, private bookmarking service dating from 2005 through 2011. I'm not looking forward to it.