This paper proposes a method for estimating and detecting optical signals in practical photon-counting receivers. There are two important aspects of non-perfect photon-counting receivers, namely, (i) dead time which results in blocking loss, and (ii) non-photon-number-resolving, which leads to counting loss during the gate-ON interval. These factors introduce nonlinear distortion to the detected photon counts. The detected photon counts depend not only on the optical intensity but also on the signal waveform, and obey a Poisson binomial process. Using the discrete Fourier transform characteristic function (DFT-CF) method, we derive the probability mass function (PMF) of the detected photon counts. Furthermore, unlike conventional methods that assume an ideal rectangle wave, we propose a novel signal estimation and decision method applicable to arbitrary waveform. We demonstrate that the proposed method achieves superior error performance compared to conventional methods. The proposed algorithm has the potential to become an essential signal processing tool for photon-counting receivers.