Traveling Late on Trains

Yes. it's perfectly safe. Do be aware that you won't be able to go DIRECTLY to Vernazza, and will have at least one if not two train changes. You'll also want to check that late-night check-in is possible at your accommodation in Vernazza? The majority of CT accommodations are small, family-run businesses without 24/7 guest services so you could run into difficulty if arriving very late at night unless arrangements are made beforehand.

I guess you should define "late night". If you are looking at the 8 pm IC train to Sestri Levante changing to the Regionale to Vernazza, I wouldn't worry. You'll have a reserved seat on the IC train.