Searches for "dark" subhaloes in gamma-ray point-like source catalogues are among promising strategies for indirect dark matter detection. Such a search is nevertheless affected by uncertainties related, on the one hand, to the modelling of the dark matter subhalo distribution in Milky-Way-like galaxies, and, on the other hand, to the sensitivity of gamma-ray instruments to the dark matter subhalo signals. In the present work, we assess the detectability of dark matter subhaloes in Fermi-LAT catalogues, taking into accounts uncertainties associated with the modelling of the Galactic subhalo population. We use four different halo models bracketing a large set of uncertainties. For each model, adopting an accurate detection threshold of the LAT to dark matter subhalo signals and comparing model predictions with the number of unassociated point-sources in Fermi-LAT catalogues, we derive upper limits on the annihilation cross section as a function of dark matter mass. Our results show that, even in the best-case scenario (i.e. DMonly subhalo model), which does not include tidal disruption from baryons, the limits on the dark matter parameter space are less stringent than current gamma-ray limits from dwarf spheroidal galaxies. Comparing the results obtained with the different subhalo models, we find that baryonic effects on the subhalo population are significant and lead to dark matter constraints that are less stringent by a factor of about 2 to 5. This uncertainty comes from the unknown resilience of dark matter subhaloes to tidal disruption.