Is the issue that the node is "blank" or the node is "not present" because that is a big difference.
Blank nodes should not pose any problem to you, and setting their value should work fine. However, null nodes (i.e. not present in the DOM) this is a "by design" issue. You can't set the value of a node that doesn't exist. First you must insert the node, then you can set its value.
From what you've stated so far, it sounds like you have an optional field or section in the view, that hasn't been inserted yet. If so, again, this is by design. First insert the field/section, then set the value.