Don't flatter yourself.

The problem Google is having isn't with storing the links, its with the effect of the links on the personalization of your search results. Which is a problem WebMynd isn't facing.

They can't precompute the eigenvectors because it changes every time you visit a web page and calculating it live for each search request when the user has thousands of personal pages can be expensive.

I would have just disabled the effect of the personalization on search of bookmarks not added manually.