Covert communication and physical layer security (PLS) have emerged as two essential pillars for safeguarding wireless networks against increasingly sophisticated eavesdropping and surveillance threats. This paper investigates a downlink hybrid power–frequency multiple access (HPMA) system aided by a friendly jammer, where a single source communicates with two legitimate users in the presence of a passive eavesdropper. By jointly exploiting the power and frequency domains, the proposed HPMA scheme achieves clear advantages in terms of covertness and secrecy performance compared to conventional orthogonal multiple access (OMA) and non-orthogonal multiple access (NOMA) schemes. For performance analysis, we derive closed-form and approximated expressions for key metrics, including detection error probability (DEP), secrecy outage probability (SOP), effective secrecy throughput (EST), and average secrecy capacity (ASC), which reveal important trade-offs among resource allocation, jammer power, and secrecy reliability. To further reduce the computational burden of conventional analysis, a regression-based deep neural network (DNN) framework is developed to efficiently predict the secrecy performance of the considered system. Extensive Monte Carlo simulations validate the analytical results and confirm the superiority of the proposed HPMA scheme with friendly jamming. These findings provide useful insights for the design of future secure and covert wireless systems with low-complexity and intelligent physical-layer security requirements.