In this paper, we propose a joint delay-Doppler estimation framework for Rydberg atomic quantum receivers (RAQRs) leveraging affine frequency division multiplexing (AFDM), as a future enabler of hyper integrated sensing and communication (ISAC) in 6G and beyond. The proposed approach preserves the extreme sensitivity of RAQRs, while offering a pioneering solution to the joint estimation of delay-Doppler parameters of mobile targets, which has yet to be addressed in the literature due to the inherent coupling of time-frequency parameters in the optical readout of RAQRs to the best of our knowledge. To overcome this unavoidable ambiguity, we propose a dual-chirp AFDM framework where the utilization of distinct chirp parameters effectively converts the otherwise ambiguous estimation problem into a full-rank system, enabling unique delay-Doppler parameter extraction from RAQRs. Numerical simulations verify that the proposed dual-chirp AFDM shows superior delay-Doppler estimation performance compared to the classical single-chirp AFDM over RAQRs.