First, the missing model data might be a result of using Detached drawings? It's not a common technique, but it would be the reason models aren't loaded when you open a drawing.
In your batch print script, find the call for OpenDoc6 and make sure you're passing the argument to load the model - swOpenDocOptions_LoadModel.
If you still need to check the note text, you can get the Note interface and use the GetText method. It will return the text value rather than the link syntax. Here's an example. You'd need to code the location of the note into the SelectByID2 method. Alternatively, you'd need to cycle through all notes on the drawing.
Dim swApp As SldWorks.SldWorks
Dim Part As ModelDoc2
Dim boolstatus As Boolean
Dim longstatus As Long, longwarnings As Long
Set swApp = Application.SldWorks
Set Part = swApp.ActiveDoc
boolstatus = Part.Extension.SelectByID2("", "NOTE", 0.376, 0.0757, 0, False, 0, Nothing, 0)
Dim sm As SelectionMgr
Set sm = Part.SelectionManager
Dim myNote As Note
Set myNote = sm.GetSelectedObject(1)
We're not using Detached Drawings. I tried using the option - swOpenDocOptions_LoadModel - and that did not make a difference. I began noticing that different computers opened the drawings with the watermark, or without the watermark consistently so I began investigating the system settings and found that most of us have the setting "Allow auto-update when opening drawings" checked. With this option checked the watermark does not show up. Additionally by adding a simple rebuild in my print macro even with this box unchecked the watermark will go away. I also spent some time with the above code to try and find the string of text and that also worked. Thanks for the help!