There seems to be a myth that all vegans are always eating soy for every single meal and snack. In my experience, this is not true. Almost every problem in those links has to do with eating massive amounts of soy. I would be willing to guess that most vegans eat less soy than the average. Most processed food is filled to the brim with soy. Most processed food is not vegan. Vegans generally eat considerably less processed food. Soy is just a small part of a huge variety of foods that vegans eat, a variety that is much larger than the Standard American Diet.

Second, most of those points are about what soy isn't. It's kinda like saying you should never ride a bus because a buses does not cure cancer, nor do buses emit a tiger contraceptive aura.

Neither of those links conclude that soy isn't safe. Rather, they state that there is a massive business interest in soy resulting in some overstated health claims.