I don't know if the scoring code has been changed, but negative score from UFO (Shipping) is -1 per 30 minutes. So it'd take a *lot* of time for ratmen to generate 4000 negative points. Each shipping (band) generates -48 points a day. I know they spawn in large numbers, but even assuming 10 bands at one time, it's still 8 days for -4000pts. I think the negative score might be from something else (conversions?), or a combination of 'something elses'.
On that note - is there a reason they even generate negative points? I'd assume it's engine limitation - can't exclude certain shipping/missions from point generation. But if it's not, I'd like to know why piratez are blamed for ratmen raids (which I assume are something of a standard in the 27th century) and in no way connected to major factions which we're supposed to be hurting.
As for hitting them - they have a lot of dodge, so unless you have a high to-hit bonus you might have crappy chances to hit. It even says so in the description of Roving Bands shipping.