Theseus' ship is not a problem for materialistic explanations of anything; it's a problem for anybody who thinks the nature of a thing is governed by the words used to describe it.

The fact that you would continue to call a ship the same after exchanging all its parts is not an ontological problem, it is a problem arising from the imprecise use of language or intention to use an approximate/aggregate notion of identity. (I would recommend studying topology for a more modern understanding of this.)