Ironically you yourself are putting TG's story in a box, imo you are wrong, being seinen or shonen has nothing to do with what happens, especially since the author doesnt seem the type to be restricted by any "cathegory".
Everything about Kaneki's family is not 100% clear yet, his father may have a role that we dont know yet, he may have had an actual reason to disappear so at this point excluding possibilities with the "shounen-excuse" is simply nonsense imo, the story could very easily go in unexpected directions.