gummby what you are describing is very very unusual.
A 13 year old girl who wets the bed almost every night needs medical help. Who knows why this is still happening, she needs medical intervention to help her control her bladder during the night, or a strategy to set her alarm clock so she can empty her bladder in the middle of the night and not pee her mattress. It's very hard to tell what's going on in that situation.
An 11 year old boy who is up until 4 a.m. waiting for his dad to go to bed is living an odd lifestyle. He needs to be in bed around 9 or so, so he gets enough sleep to function in school. He can't possibly function as a student if he is going to bed at 4 a.m.
"Acceptance" of child neglect isn't necessarily a good thing, and I don't believe Buddhism teaches turning a blind eye to child neglect.
You are right to bring these concerns to this forum - I know you don't have any kids so it's probably hard for you to know how neglectful this situation truly is - but it's good that you are asking for help.
Someone needs to get through to the boyfriend and his ex wife that this it is terrible for the kids to ignore this situation. If they don't listen to you, you should arrange for a family therapist to come talk with you, your boyfriend, and his ex. Your job is to explain what you are seeing in non-judgmental terms and then to be quiet (or even leave), and then the therapist should be ready to explain to the parents of these kids that: 1) this is not a normal way to raise a 13-year-old and 11-year-old, 2) it should not be treated as just an alternative lifestyle or ignored, and 3) it is really bad for the kids, to let it continue. You said you think there is something going on, my guess is that this is the way they gave in, years ago, on bedtime fights (the kind that begin at age 2 or 3, when a child simply does not want to go to bed at bedtime and puts up a fuss), and they have now let it slide so long that they don't want to face it. But whatever reason it's happening, it needs to be addressed.
My first sentence is confusingly said. I meant, "that it is terrible for the kids if the parents ignore this situation."