Yes, indeed, there is a strong risk for bubbles. In order to deter bubbles, there must still be a healthy social fabric and network applications that promote and incentivize cross-cultural interaction and knowledge sharing. That's a social, political, design & technical challenge.

Also...

I'm imagining the possibility "encrypted queries" between trusted parties. You could allow people to send you a search query that is encrypted in some way such that you couldn't read it, but you could still run it on your local index and send them back a result. Storing not only your own well-structured index but numerous other parties indices as well could be way too expensive. Instead, it makes sense only to maintain a relatively small local index for when you're truly offline. But to allow others to search your index anonymously, perhaps in exchange for the ability to search theirs anonymously. You could let trusted parties search your content without actually revealing their search terms, which may contain sensitive terms, like "cancer" or "schizophrenia symptoms". Maybe this could be done in a way that also obscures who actually ran the query. This sounds like a challenge for zero-knowledge proofs and some kind of anonymous traffic routing system.

In practice, it'd be like a hybrid of anonymous distributed routing and anonymous distributed search.