Should I inform about an updated CV post deadline? (CS PhD USA)
Should I send the places I applied an e-mail saying that the paper which was in review (and mentioned in my SOP/LOR/CV) got accepted?

No. Your CV/application is a snapshot in time, institutes likely won't update your CV/application, and they don't need such an additional burden. (Especially after two months, institutes are likely nearing or have made decisions.)

Does it have any effect on their decision?

It would improve your CV/application, equally it may annoy the institutes: It may have a positive or negative impact.