YANBU to worry but I think you would be unreasonable to stop her going. It is good if she is aware you are worried though as I think that will probably make her more aware of the risks and be more cautious!
I went inter-railing when I was 18 and had no problems at all with the night trains. In addition to inter railing I travelled a lot as a child (with parents!) and adult around Europe by night train (France, Spain, Germany, Bosnia, Serbia, Croatia, Czech Republic, Slovakia) as well as a couple of others countries further afield and have never had any problems on the night trains.
The only issue we had the whole time inter railing was on a Paris train station platform at about 10pm. It wasn't trouble as such but a man tried to talk to our group and it made us uneasy as something didn't feel right. We were very cautious so picked up on if straight away that something wasn't right and had our wits about us.
Many times I've woken up in the middle of the night on the trains, looked out the window to see which station we are at and the station will be packed. I guess this is because the night time stops are busy city stations or interchanges rather than smaller surburban ones.
Are the stories you've heard first hand experiences or things you've read online or been told by other people who know a friend of a friend? My most recent train travels have been to an Asian country and there's a lot you read about train travel there not being safe. I've never had any problems at all.
If your daughter is aware of the risks, takes a few precautions with her valuables and is sensible then she will more than likely be safe.
If you want any tips for her then send me a message and I'll be happy to help.