They left a lot of ambiguities with her, and it frustrated me at the time. I definitely think they wanted us to believe Valentin had something to do with her death, if there even WAS a death. Valentin was pulling out all the stops to win Nina back, and he mentioned at the time how Madeline kept hurting Nina even from behind bars (trying to get Nina and/or Maxie to help her get paroled by pretending to be repentant), only to have news of her death come within the next episode or two. I'm not sure but I think he visited her in prison shortly before that, too. The autopsy said she died of a heart attack, but Liesl swore up and down that her sister was in perfect health and wanted there to be further investigation. There wasn't, obviously--the scenes were more about planting doubts in the viewers' minds than actually advancing a plot. I thought at the time that Valentin could have pulled strings to get her released from prison, faked her death and paid her off to leave the country and never contact Nina again. This would have allowed Donna Mills to return and stir up trouble when/if she wanted. I had to give up that dream when it was stated later on (via ret-con) that Liesl saw Valentin take a DNA sample from Madeline as she laid in the coffin (which...ick), the DNA he used to fake the Nina/Sasha maternity tests. By this point I decided they must have moved on from Madeline (and Mills), so I'm resigned to not seeing her back again. And even if Valentin did have her killed in prison, they've moved on and won't bring it up again. Madeline's last (and only) champion, Liesl, is currently being tried at the Hague (!!) so she's got other things to worry about.
One thing I will continue to hold onto, however, is the box Nina received after Madeline's death that contained the necklace that links Nina to her baby. The letter (supposedly from Madeline) said the baby was given the other half of the necklace, implying the now-adult child would still have the other half. What if someone else was behind that whole thing, and the necklace (now seen in Nelle's possession) is no more a link to the baby than that bogus DNA test? Madeline never struck me as the sentimental type, especially in that period where she poisoned Nina to kill that baby, and framed Silas for the crime. She went to extreme lengths to make sure Silas never knew about the baby and could never find Nina as she languished in that coma. If the family found out Nina had given birth to an heir/heiress, Madeline's claim to the fortune would have been undermined further, so getting rid of (adopting out) the baby and not leaving any path to finding him/her was vital. The idea that such a heinous woman would leave an evidence trail of her crimes via a necklace doesn't stand up to the smell test. I can't pin the "box from Madeline" on Valentin, though, because if he had created the two necklaces, he would have given the other one to Sasha to wave around and reinforce the idea she was the baby.
I'm just desperate to ditch the whole "Nelle is Nina's daughter" plotline, so I'll be glad to make the necklace thing into a hoax by any means necessary.