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RAW seem to indicate that there is a benefit to over-running naval units in a surprise impulse, i.e. more likely to be captured or destroyed (15.1) but other than a referral to the over-run rules there is no indication of how this works.

Is it maybe a -1 DRM?

IMO the advantage consists of the fact that you don't need to have them disorganized to be able to overrun them.

Overrunning naval units
If a land unit from the other side moves into a port containing any of your naval units, they must rebase. Before they do, roll for each face-down or surprised naval unit there.

Yes that's it. Disorganized anytime they suffer the overrun rolls, but even not disorganized, they also suffer them in a surprise impulse. Likewise organized aircraft overrun when surprised are eliminated.