Recent analyses of small collision systems, namely $p+p$ and $p+$Pb at the LHC and $p+$Au, $d+$Au and $^{3}$He+Au at RHIC, have revealed azimuthal momentum anisotropies commonly associated with collective flow in larger systems. Viscous hydrodynamics and parton cascade calculations have proved successful at describing some flow-like observables in these systems. These two classes of calculations also confirm these observables to be directly related to the initial geometry of the created medium. However, the question of whether equilibrium dynamics is the dominant driver of the signal remains open, given the short lifetime of small systems. In this regime, pre-equilibrium dynamics and late stage hadronic interactions are expected to play a significant role. Hence, a beam energy scan of small systems---that amounts to varying the initial temperature and the lifetime of the medium---can provide valuable information to shed light on these issues. In this paper, we present predictions from viscous hydrodynamics (SONIC), partonic (AMPT) and hadronic (UrQMD) cascade calculations for elliptic $v_2$ and triangular $v_3$ anisotropy coefficients in $d$+Au at $\sqrt{s_{NN}}$ = 7.7, 20, 39, 62.4 and 200 GeV, corresponding to the expected running at RHIC in 2016. We also present predictions for $d$+Pb at $\sqrt{s_{NN}}$ = 5.02 TeV, an interesting system to compare to existing $p+$Pb data taken at the LHC.