Existing defensive deception (DD) approaches apply game theory, assuming that an attacker and defender play the same, full game with all possible strategies. However, in deceptive settings, players may have different beliefs about the game itself. Such structural uncertainty is not naturally handled in traditional game theory. In this work, we formulate an attackdefense hypergame where multiple advanced persistent threat (APT) attackers and a single defender play a repeated game with different perceptions. The hypergame model systematically evaluates how various DD strategies can defend proactively against APT attacks. We present an adaptive method to select an optimal defense strategy using hypergame theory for strategic defense as well as machine learning for adaptive defense. We conducted in-depth experiments to analyze the performance of the eight schemes including ours, baselines, and existing counterparts. We found the DD strategies showed their highest advantages when the hypergame and machine learning are considered in terms of reduced false positives and negatives of the NIDS, system lifetime, and players' perceived uncertainties and utilities. We also analyze the Hyper Nash Equilibrium of given hypergames and discuss the key findings and insights behind them.