Recent evolutions in semiconductors have brought the terahertz band in the spotlight as an enabler for terabit-per-second communications in 6G networks. Most of the research so far, however, has focused on understanding the physics of terahertz devices, circuitry and propagation, and on studying physical layer solutions. However, integrating this technology in complex mobile networks requires a proper design of the full communication stack, to address link- and system-level challenges related to network setup, management, coordination, energy efficiency, and end-to-end connectivity. This paper provides an overview of the issues that need to be overcome to introduce the terahertz spectrum in mobile networks, from a MAC, network and transport layer perspective, with considerations on the performance of end-to-end data flows on terahertz connections.