I guess that you get suffix "_Model", when you use modeling template in File/New. I suspect, then when you use assembly template in File/New, you get something else. Maybe "_ASSM".
Maybe this is what has happened with those sub-assemblies:
1. click on file/new and select modeling template (let's say by mistake). You Will get the "_Model" suffix
2. click on Add Component and add some components into this file.
3. You have created assembly structure. There is no solids or any other geometry in this file. Part Navigator is empty.
NX does allow creating assembly structure, even if you select Modeling template. And I guess, this is what has happened to those sub-assembly files.
The same can happen, when you use Create New Component in an assembly file. You can select Modeling template for creating new component. Then, set this new component as work and create new component or add component into this one. Doing so, you have created the sub-assembly out of model file.
Of course, those names can be changed later (rename or save as, etc.)
And if you don't want to have anything like _Model being added to the file name, you can set this in customer defaults (gateway/general/file new tab).
I hope that this explains correctly, what you are looking for.