Cooperative Adaptive Cruise Control (CACC) systems have the potential to increase roadway capacity and mitigate traffic congestion thanks to the short following distance enabled by inter-vehicle communication. However, due to limitations in acceleration and deceleration capabilities of CACC systems, deactivation and switch to ACC or human-driven mode will take place when conditions are outside the operational design domain. Given the lack of elaborate models on this interaction, existing CACC traffic flow models have not yet been able to reproduce realistic CACC vehicle behaviour and pay little attention to the influence of system deactivation on traffic flow at bottlenecks. This study aims to gain insights into the influence of CACC on highway operations at merging bottlenecks by using a realistic CACC model that captures driver-system interactions and string length limits. We conduct systematic traffic simulations for various CACC market penetration rates (MPR) to derive free-flow capacity and queue discharge rate of the merging section and compare these to the capacity of a homogeneous pipeline section. The results show that an increased CACC MPR can indeed increase the roadway capacity. However, the resulting capacity in the merging bottleneck is much lower than the pipeline capacity and capacity drop persists in bottleneck scenarios at all CACC MPR levels. It is also found that CACC increases flow heterogeneity due to the switch among different operation modes. A microscopic investigation of the CACC operational mode and trajectories reveals a close relation between CACC deactivation, traffic congestion and flow heterogeneity.