Yeah indexing will be harder, unless the client breaks it down and queries by a set of pubkeys directly. But for that to happen, relays must abandon the filter limits they have today.
Essentially, they will have to go develop a function in say SQL that assesses if a pubkey is inside the set of an xpub or not. Key derivation is heavy, so maybe there must be a new xpub crypto scheme that makes it easier for indexing.