The design of Apache Kafka systems involves configuring parameters such as replication factor, batch size, linger.ms, compression type, acks configuration, and consumer group settings to achieve high throughput while bounding end-to-end latency. The goal is to minimize the impact of replication overhead on commit time and reduce queueing delays. By monitoring and tuning client configurations, scaling brokers, and optimizing batching, developers can ensure that their Kafka systems meet application requirements for both throughput and latency.