Self-organized laser functionalization using femtosecond laser pulses enables hierarchical micro/nano-scale structure formation on silicon device surfaces. However, in thin wafers, deep valley formation and local through-hole generation can create transmission pathways that pose risks to backside circuitry or adjacent device layers. Here, we investigate transmission-induced damage in 200 µm thick silicon wafers processed with a focused 1030 nm, 175 fs laser beam at different fluences and pulse counts. A second silicon wafer was placed behind the processed wafer to evaluate damage caused by transmitted laser energy. Although laser scanning confocal microscopy showed that the average valley depth could remain below the wafer thickness, backside SEM revealed local through-hole formation at higher fluence and pulse-count conditions. For example, at 9.16 J/cm² and a pulse count of 770, the measured average valley depth was approximately 187 µm, while backside through-holes were still observed. Stacked-wafer experiments and Raman analysis confirmed that these through-holes can transmit sufficient laser energy to damage a second silicon wafer with structural modification and residual stress around the damaged regions, suggesting that damage on the second wafer may be enhanced by mechanical or thermomechanical coupling between the wafers. Cross-sectional SEM revealed tapered, curved, inclined, and partially covered valleys, explaining why top-down optical measurements can underestimate the deepest local features. These results show that safe femtosecond laser functionalization of thin Si wafers requires evaluation of local maximum valley depth, through-hole formation, backside damage, and transmission effects in addition to conventional surface-height measurements.