Just to let you know, if it can help someone else, we have find the root cause of the problem.
We were using node.store.allow_mmap: false in the configuration of our Elasticsearch cluster deployment file and this was the reason behind the high system CPU.
This was clear in the documentation:
For production workloads, it is strongly recommended to increase the kernel setting vm.max_map_count to 262144 and leave node.store.allow_mmap unset.