The vast increase of IoT technologies and the ever-evolving attack vectors and threat actors have increased cyber-security risks dramatically. Novel attacks can compromise IoT devices to gain access to sensitive data or control them to deploy further malicious activities. The detection of novel attacks often relies upon AI solutions. A common approach to implementing AI-based IDS in distributed IoT systems is in a centralised manner. However, this approach may violate data privacy and secrecy. In addition, centralised data collection prohibits the scale-up of IDSs. Therefore, intrusion detection solutions in IoT ecosystems need to move towards a decentralised direction. FL has attracted significant interest in recent years due to its ability to perform collaborative learning while preserving data confidentiality and locality. Nevertheless, most FL-based IDS for IoT systems are designed under unrealistic data distribution conditions. To that end, we design an experiment representative of the real world and evaluate the performance of two FL IDS implementations, one based on DNNs and another on our previous work on DBNs. For our experiments, we rely on TON-IoT, a realistic IoT network traffic dataset, associating each IP address with a single FL client. Additionally, we explore pre-training and investigate various aggregation methods to mitigate the impact of data heterogeneity. Lastly, we benchmark our approach against a centralised solution. The comparison shows that the heterogeneous nature of the data has a considerable negative impact on the model performance when trained in a distributed manner. However, in the case of a pre-trained initial global FL model, we demonstrate a performance improvement of over 20% (F1-score) when compared against a randomly initiated global model.