Drones are a promising technology performing various functions, ranging from aerial photography to emergency response, requiring swift fault diagnosis methods to sustain operational continuity and minimise downtime. This optimises resources, reduces maintenance costs, and boosts mission success rates. Among these methods, traditional approaches such as visual inspection or manual testing have long been utilised. However, in recent years, data representation methods, such as deep learning systems, have achieved significant success. These methods learn patterns and relationships, enhancing fault diagnosis, but also face challenges with data complexity, uncertainties, and modelling complexities. This paper tackles these specific challenges by introducing an efficient representation learning method denoted Multiverse Augmented Recurrent Expansion (MVA-REX), allowing for an iterative understanding of both learning representations and model behaviours and gaining a better understanding of data dependencies. Additionally, this approach involves Uncertainty Bayesian Optimisation (UBO) under Extreme Learning Machine (ELM), a lighter neural network training tool, to tackle both uncertainties in data and reduce modelling complexities. Three main realistic datasets recorded based on acoustic emissions are involved in tackling propeller and motor failures in drones under realistic conditions. The UBO-MVA Extreme REX (UBO-MVA-EREX) is evaluated under many, error metrics, confusion matrix metrics, computational cost metrics, and uncertainty quantification based on both confidence and prediction interval features. Application compared to the well-known long-short term memory (LSTM), under Bayesian optimisation of the approximation error, demonstrates performances, certainty, and cost efficiency of the proposed scheme. More specifically, the accuracy obtained by UBO-MVA-EREX, ~0.9960, exceeds the accuracy of LSTM, ~0.9158, by ~8.75%. Besides, the search time for UBO-MVA-EREX is ~0.0912 s, which is ~98.15% faster than LSTM, ~4.9287 s, making it highly applicable for such challenging tasks of fault diagnosis-based acoustic emission signals of drones.