In this work, the optimization of the analog transmit waveform for joint delay-Doppler estimation under sub-Nyquist conditions is considered. Based on the Bayesian Cramér-Rao lower bound (BCRLB), we derive an estimation theoretic design rule for the Fourier coefficients of the analog transmit signal when violating the sampling theorem at the receiver through a wide analog pre-filtering bandwidth. For a wireless delay-Doppler channel, we obtain a system optimization problem which can be solved in compact form by using an Eigenvalue decomposition. The presented approach enables one to explore the Pareto region spanned by the optimized analog waveforms. Furthermore, we demonstrate how the framework can be used to reduce the sampling rate at the receiver while maintaining high estimation accuracy. Finally, we verify the practical impact by Monte-Carlo simulations of a channel estimation algorithm.