Secondary-electron (SE) emission in the helium ion microscope (HIM) becomes sensitive to membrane thickness when the sample is thin enough for He-ion transmission and when the SEs emitted from the bottom surface are collected. We correlated the total SE intensity of suspended, nanometer-thick MoS₂ flakes on lacey carbon with thickness measured independently by electron energy-loss spectroscopy. The response peaks at 40-55 nm, with an apparent back-to-front SE signal ratio reaching 4.7. The peaked, thickness-dependent component is attributed primarily to SE emission at the bottom surface of the flake, rather than to transmitted ions striking instrument surfaces. Applying SRIM ionization profiles, an asymmetric SE-escape model with a longer escape depth on the exit side reproduces the response. We find an effective exit-side escape depth of approximately 10 nm, five times the assumed 2 nm entrance value, suggesting that deposited energy reaches the exit surface far more efficiently than the entrance surface or that the SRIM model's energy deposition profile is shifted by an effect such as channeling. The correlation provides a rapid thickness screen for suspended membranes and a route to testing low-energy ion-solid interaction models in thin materials.