To represent the means of a two random variables $X_1, X_2$, should the bar also cover the subscript, i.e.
should it be $$\overline{X_1},\overline{X_2}$$ or $$\overline{X}_1,\overline{X}_2$$
and why?
The first option seems to be the logical choice but the second option looks neater.
Addendum: If we decided that the first option is the appropriate one, what would the second option then represent?

In this situation, the first option certainly seems more “logical,” i.e. you can interpret its meaning right away.
However, you can also justify the second by considering $X$ to be tuple of two random variables (with components $X_1$ and $X_2$) and the mean of the tuple to be the tuple $\overline{X}$ with components $$ \overline{X}_i = \overline{X_i} $$ for every relevant index $i$ (i.e. $i \in \{1, 2\}$). This is what I would expect the second notation to denote – so the second would really be the same as the first.
After all, considering their visual similarity, it would almost seem malicious to use them for different things.