We show how exclusive vector meson production off light ions can be used to probe the spatial distribution of small-$x$ gluons in the deuteron and $^3$He wave functions. In particular, we demonstrate how short range repulsive nucleon-nucleon interactions affect the predicted coherent $J/\Psi$ production spectra... Fluctuations of the nucleon substructure are shown to have a significant effect on the incoherent cross section above $|t|\gtrsim 0.2\,\mathrm{GeV}^2$. By explicitly performing the JIMWLK evolution, we predict the $x$-dependence of coherent and incoherent cross sections in the EIC energy range. Besides the increase of the average size of the nucleus with decreasing $x$, both the growth of the nucleons and subnucleonic hot spots are visible in the cross sections. The decreasing length scale of color charge fluctuations with decreasing $x$ is also present, but may not be observable for $|t|<1\,\mathrm{GeV}^2$, if subnucleonic spatial fluctuations are present. (read more)