Many important properties of cyber-physical systems (CPS) are defined upon the relationship between multiple executions simultaneously in continuous time. Examples include probabilistic fairness and sensitivity to modeling errors (i.e., parameters changes) for real-valued signals. These requirements can only be specified by hyperproperties. In this work, we focus on verifying probabilistic hyperproperties for CPS. To cover a wide range of modeling formalisms, we first propose a general model of probabilistic uncertain systems (PUSs) that unify commonly studied CPS models such as continuous-time Markov chains (CTMCs) and probabilistically parametrized Hybrid I/O Automata (P2HIOA). To formally specify hyperproperties, we propose a new temporal logic, hyper probabilistic signal temporal logic (HyperPSTL) that serves as a hyper and probabilistic version of the conventional signal temporal logic (STL). Considering complexity of real-world systems that can be captured as PUSs, we adopt a statistical model checking (SMC) approach for their verification. We develop a new SMC technique based on the direct computation of the significance levels of statistical assertions for HyperPSTL specifications, which requires no a priori knowledge on the indifference margin. Then, we introduce SMC algorithms for HyperPSTL specifications on the joint probabilistic distribution of multiple paths, as well as specifications with nested probabilistic operators quantifying different paths, which cannot be handled by existing SMC algorithms. The effectiveness of our SMC algorithms is shown on CPS benchmarks with varying levels of complexity, including the Toyota Powertrain Control System (https://github.com/Mojzaar/Benchmarks).