  Exoplanet emission spectra are often modelled assuming that the hemisphere
observed is well represented by a horizontally homogenised atmosphere. However
this approximation will likely fail for planets with a large temperature
contrast in the James Webb Space Telescope (JWST) era, potentially leading to
erroneous interpretations of spectra. We first develop an analytic formulation
to quantify the signal-to-noise ratio and wavelength coverage necessary to
disentangle temperature inhomogeneities from a hemispherically averaged
spectrum. We find that for a given signal-to-noise ratio, observations at
shorter wavelengths are better at detecting the presence of inhomogeneities. We
then determine why the presence of an inhomogeneous thermal structure can lead
to spurious molecular detections when assuming a fully homogenised planet in
the retrieval process. Finally, we quantify more precisely the potential biases
by modelling a suite of hot Jupiter spectra, varying the spatial contributions
of a hot and a cold region, as would be observed by the different instruments
of JWST/NIRSpec. We then retrieve the abundances and temperature profiles from
the synthetic observations. We find that in most cases, assuming a homogeneous
thermal structure when retrieving the atmospheric chemistry leads to biased
results, and spurious molecular detection. Explicitly modelling the data using
two profiles avoids these biases, and is statistically supported provided the
wavelength coverage is wide enough, and crucially also spanning shorter
wavelengths. For the high contrast used here, a single profile with a dilution
factor performs as well as the two-profile case, with only one additional
parameter compared to the 1-D approach.
