I see most of the applied econometrics papers using the two-way fixed effects model, controlling for time and units fixed effects, so: $$y_{it}=\alpha_{i}+ \gamma_{t} +\beta x_{it} +\epsilon_{it}$$ I understand the reasoning behind it.
I would like to know if there are situations when we should not control for unit-fixed effects for some reason. For instance, suppose I have a panel with 500 units across 10 time periods. By controlling for unit-fixes effects I loose 500 degrees of freedom, right? Is it still better than not controlling? As an example I found this paper with similar setup (they include a spatial covariate, but it doesn't matter for this point). Their main model is a panel regression (640 units across 12 time periods) controlling for time-fixed effects only.