Integrated sensing and communication (ISAC) has emerged as a key enabler for next-generation wireless networks, supporting advanced applications such as high-precision localization and environment reconstruction. Cooperative ISAC (CoISAC) further enhances these capabilities by enabling multiple base stations (BSs) to jointly optimize communication and sensing performance through coordination. However, CoISAC beamforming design faces significant challenges due to system heterogeneity, large-scale problem complexity, and sensitivity to parameter estimation errors. Traditional deep learning-based techniques fail to exploit the unique structural characteristics of CoISAC systems, thereby limiting their ability to enhance system performance. To address these challenges, we propose a Link-Heterogeneous Graph Neural Network (LHGNN) for joint beamforming in CoISAC systems. Unlike conventional approaches, LHGNN models communication and sensing links as heterogeneous nodes and their interactions as edges, enabling the capture of the heterogeneous nature and intricate interactions of CoISAC systems. Furthermore, a graph attention mechanism is incorporated to dynamically adjust node and link importance, improving robustness to channel and position estimation errors. Numerical results demonstrate that the proposed attention-enhanced LHGNN achieves superior communication rates while maintaining sensing accuracy under power constraints. The proposed method also exhibits strong robustness to communication channel and position estimation error.