Abstract HyperSurfaces (HSFs) comprise structurally reconfigurable metasurfaces whose electromagnetic properties can be changed via a software interface, using an embedded miniaturized network of controllers, enabling novel capabilities in wireless communications, including 5G applications. Resource constraints associated with a hardware testbed of this breakthrough technology, currently under development, necessitate an interconnect architecture of a Network of Controllers (CN) that is distinct from, yet reminiscent to, those of conventional Network-on-Chip (NoC) architectures. To meet the purposes of our HSF testbed, we rationalize the construction of an irregular topology where its controllers are interconnected in a Manhattan-like geometry, with the flow of control directives conducted in a handshaking mode, and routing operated by an XY-YX algorithm that is agnostic of the CN connectivity, determined following the results of model specification and model checking techniques. With such controllers prone to the appearance of permanent faults, threatening the operation of such HSFs, we propose, develop and evaluate two fault adaptive routing algorithms aiming to enhance the successful delivery of packetized control directives to their recipients: (1) Loop Free Algorithm (LFA), and (2) Reliable Delivery Algorithm (RDA) of deterministic and probabilistic variants. LFA and RDA are developed based on utilizing said topology-agnostic XY-YX routing algorithm as a base, along with an appropriate adoption of routing turn rules, to address said HSF CN challenges that deviate from traditional fault tolerant routing algorithms seen in NoCs. Experimental evaluation results obtained using a custom developed simulator, show that probabilistic RDA exhibits top performance in terms of successful packet delivery ratio and topology coverage, albeit at the expense of a higher path hop count. Pointers in addressing tradeoffs between HSF CN performance and resource utilization are also provided.