They won't be, short answer. EES registration is not required for round-trip cruises starting and ending outside Schengen ports if they only stop in Schengen.
See the presentation here, from the CLIA. The plan is to only register stop outside Schengen or on one-way cruises, where people are entering and staying within Schengen. For all other itinerates, it will be done based on a risk basis. Lines already need to report missing passengers to local authorities, so the risk of someone entering and staying in the zone off a round-trip cruise is already minimal.