Cardinality Estimation (CE) for query is to estimate the number of results without execution, which is an effective index in query optimization. Recently, CE over has achieved great success in knowledge graphs (KGs) that consist of triple facts. To more precisely represent facts, current researchers propose hyper-relational KGs (HKGs) to represent a triple fact with qualifiers, where qualifiers provide additional context to the fact. However, existing CE methods over KGs achieve unsatisfying performance on HKGs due to the complexity of qualifiers in HKGs. Also, there is only one dataset for HKG query cardinality estimation, i.e., WD50K-QE, which is not comprehensive and only covers limited patterns. The lack of querysets over HKG also becomes a bottleneck to comprehensively investigate CE problems on HKGs. In this work, we first construct diverse and unbiased hyper-relational querysets over three popular HKGs for investigating CE. Besides, we also propose a novel qualifier-attached graph neural network (GNN) model that effectively incorporates qualifier information and adaptively combines outputs from multiple GNN layers, to accurately predict the cardinality. Our experiments illustrate that the proposed hyper-relational query encoder outperforms all state-of-the-art CE methods over three popular HKGs on the diverse and unbiased benchmark.