Cosmology is at a crossroads. Experiments are providing an unprecedented amount of data that, in theory, should lead to clear solutions to the many open questions in cosmology. However, with new data comes new questions and recently uncovered tensions between the predictions of the standard model of cosmology and observations are leading some to question the very foundations on which the standard model is built. To explore the vast cosmological landscape, numerical simulations are often employed, but given the broad parameter space that needs to be explored other faster (but more approximate) methods need to be adopted to maximise the coverage and the possible extensions surveyed. In this panorama one of the options is the halo model, a simple and elegant way to study the clustering of matter in the Universe. However, this method is not free from assumptions and associated uncertainties. In this thesis I explore the uncertainties associated with the halo model making use of cosmological numerical simulations. I use the BAHAMAS simulations to obtain data products such as the mass density profiles of the haloes and the number density of haloes over a wide range of masses and I use these quantities in the halo model formalism in order to make a self-consistent comparisons against the simulations results. Aside from this application, I calibrate a fitting function on the Einasto function, which has been shown to be a good representation of the matter distribution inside haloes, and I use a standard form for the halo mass function. Comparing against the simulation matter power spectrum at different redshift, I show the accuracy of the halo model predictions is strongly dependent on the mass definitions used with differences over 50%. In particular, the transition region between the 1-halo and the 2-halo terms and in the smallest scales sampled (k≈ 10 h/Mpc). This picture applies to both collisionless and hydrodynamical simulations, where galaxy formation processes are taken into account. In contrast to the poor ability in reproducing the matter clustering, the halo model can reproduce the relative impact of baryons on the matter clustering to a competitive accuracy (<5%) in line of next-generation observations predictions. In the second part of this work, I analyse the halo model applications of large-scale structure observables as gravitational weak lensing and thermal Sunyaev-Zel'Dovich effect. To explore these observables, I have built the halo model using the electron pressure inside haloes (relevant for the tSZ effect), and I have made several realisations of the matter power spectrum up to z=3 for the lensing observables, in both the collisionless and hydrodynamical cases. In this analysis, I have compared against observational data (e.g., KiDS-450 survey and Planck) and results obtained from light-cones from the BAHAMAS simulations. I examined the dependence of the results on the different mass definitions and the baryonic effects, in particular the baryonic suppression that can be inferred from this set of observables