C# system attributes

Question

The .NET file classes generally have no problem accessing files with the hidden or system  attributes even if such files don't show up in (normal) directory listings. 
Thus they are apparently .net files that have the hidden or system attributes. Thus can you explain to me more about these attributes?
Do these files affect code that I am writing? Could these hidden files somehow change the logic that is intended to occur in the code that is obvious to us?

Basically my question is, can these files some affect code that I am writing in the main console, desktop, and/or web application files? If so, can you explain to me how these files can affect the code that is obvious to me? The code that is contained within the