Serato Cue Storage Format - Holzhaus/mixxx GitHub Wiki
At least for MP3 files, Serato stores cue points in the ID3 v 2.3 GEOB tags of the music files. Source
The format of this binary blob has been partially documented in this blog post.
https://bugs.launchpad.net/mixxx/+bug/741613
See also serato_database_format.