The practical channel estimation for pinching-antenna networks is investigated, in which an electromagnetic-compliant in-waveguide transmission model is exhibited, incorporating bidirectional power splitting, cumulative power leakage, and waveguide attenuation. Based on this model, the paper investigates two antenna activation protocols for channel estimation: a serial protocol based on one-by-one antenna activation and a parallel protocol utilizing a binary S-Matrix activation. The serial protocol is characterized by its superior numerical stability but a lack of array gain, whereas the parallel protocol theoretically offers array gain but suffers from severe performance degradation due to structural crosstalk from the non-orthogonal S-Matrix and ill-conditioning from cumulative leakage. Furthermore, the paper analyzes the fundamental commonalities and asymmetries between uplink and downlink channel estimation in pinching-antenna systems. Numerical results demonstrate that 1) in an ideal lossless model, the parallel protocol is superior to the serial protocol due to the array gain from simultaneous energy collection in uplink transmission; 2) in a practical model with physical losses, the serial protocol outperforms the parallel protocol, as the performance of the parallel protocol is degraded by the numerical instability from cumulative leakage, which outweighs the benefit of array gain; 3) For downlink channel estimation, the serial protocol is more suitable because its strategy of concentrating the entire power budget on one measurement, while the parallel protocol is more suitable for the uplink as it can make full use of array gain.