Identifying assumptions in a research article
There is no clear way to distinguish hidden assumptions, but let's discuss your example (I'm unfamiliar with the field): 


  open source operating systems are more secure than propriety operating systems


Some possibilities:


The author makes an assumption here. It can be, e.g., based on their personal experience, or justified by some common sense.
The community makes an assumption. This may be a generally accepted assumption, but nobody has actually done research on it.
This is a generalization / rule of thumb which usually holds true.
This is a well known fact, so old or trivial that nobody bothers to cite it anymore.


I usually consider all nontrivial statements as assumptions/hypotheses/conjectures unless I find evidence to the contrary.