The telecommunication networks have become an indispensable part of our everyday life, providing support for such important areas as business, education, health care, finances, entertainment and social life. Alongside their continuous and uninterrupted operation is required while numerous new threats and attack scenarios emerge. The international security organisations warn against increasing likelihood of nuclear weapon or electro-magnetic pulse (EMP) attacks, which can be extremely harmful also for transport networks. On that background, we study efficient design of network resilient to EMP attack wherein the required protection level is provided by the application of multipath routing and military grade bunkers (advanced electro-magnetic radiation resilient approaches protecting whole network node) implementation. Formally, we define and study problem of bunkers location, routing and spectrum allocation (BLRSA) in elastic optical network (EON). In the problem objective we address two criteria - network resilience (measured by the average lost flow per potential attack) and spectrum usage. For that problem we propose integer linear programming (ILP) model and two dedicated heuristics - 1S-RSA and 2S-RSA. Then, we perform extensive numerical experiments divided into three parts: (i) tuning of the proposed approaches, (ii) comparison with reference methods, (iii) realistic case study - efficient EMP-resilient network design. In the case study we analyze benefits and costs of the proposed protection scheme. Moreover, we also analyze vulnerabilities of three realistic network topologies to EMP attacks and identify their critical nodes. The investigation proves high efficiency of the proposed approaches and shows that they allow to save up to 90% of traffic lost in the case of no protection against these types of attacks.