A comparative analysis of structural and flow-based approaches to study the vulnerability of complex network systems (NS) from targeted attacks and non-target lesions of various types is carried out. Typical structural and functional scenarios of successive targeted attacks on the most important by certain criteria system elements are considered, and scenarios of simultaneous group attacks on the overriding NS's components are proposed. The problem of system lesions scale from heterogeneous negative influences is investigated. It was confirmed that the flow-based approach allows us to obtain a much more realistic picture of such lesions consequences. It is shown that the scenarios of group targeted attacks built on the basis of NC flow model are more optimal from the point of view of selecting attack targets than structural ones.