Quantum-augmented networks aim to use quantum phenomena to improve detection and protection against malicious actors in a classical communication network. This may include multiplexing quantum signals into classical fiber optical channels and incorporating purely quantum links alongside classical links in the network. In such hybrid networks, quantum protocols based on single photons become a bottleneck for transmission distances and data speeds, thereby reducing entire network performance. Furthermore, many of the security assumptions of the single-photon protocols do not hold up in practice because of the impossibility of manufacturing single-photon emitters. Multi-photon quantum protocols, on the other hand, are designed to operate under practical assumptions and do not require single photon emitters. As a result, they provide higher levels of security guarantees and longer transmission distances. However, the effect of channel and device noise on multiphoton protocols in terms of security, transmission distances, and bit rates has not been investigated. In this paper, we focus on channel noise and present our observations on the effect of various types of noise on multi-photon protocols. We also investigate the effect of topologies such as ring, star, and torus on the noise characteristics of the multi-photon protocols. Our results show the possible advantages of switching to multi-photon protocols and give insights into the repeater placement and topology choice for quantum-augmented networks.