The adhesions are internal, and yes, unfortunately each time you have any surgery you run the risk of having adhesions, and depending on where they are, they can cause pain and/or damage. The ileostomy is not the cause of the adhesions/blockage, the surgery is.
The only one who can answer your questions are your neices doctors. It's a catch 22, they may have to do surgery to fix the blockage, but any surgery to fix adhesions can cause more.
Good luck to your neice, I know it's hard, but trust her surgeons/doctors to do what's best for her, of course she should be well informed each step of the way.
Keep us posted on what they decide