Well it's currently quite new and immature. I've said for a while that a decent system for searching the fediverse would be search engines maintaining their own instances purely for indexing purposes. They would retrieve posts via default federation, and if an instance wants to opt out of a given search engine, it's as simple as defederating from that instance. They would also ideally provide links that users can open on their home instances.

This is more a scale and mainstreaming issue than a federation issue. Once the fediverse is big enough major search engines will have to adapt or be left behind.