To quote different commenters from the deleted duplicate, as the comments are not merged:
In general it is context dependent. If, as you say, context here suggests the first then it is the first for this specific case. If a different context suggests it should be the other then it is the other there. If context is unclear then it is ambiguous. Ideally nothing should have been written in an ambiguous way and it should have been $(W_{(k,\cdot)})^T$ or similar to make it clear.
The author of that article could have clarified the order of the operations with little effort. I tend to stop reading low quality literature that give me such unnecessary headaches.
Math notation, no matter how basic, is not equivalent to programming. We are humans and not compilers. That paper is a piece of crap.
Everyone can have their own opinion about a given paper. Let's not get sidetracked by secondary questions. Reading this paragraph before the author's equation $$\mathbf{h}=\mathbf{W}^\top\mathbf{x}=\mathbf{W}^\top_{(k,\,.\,)}$$
again: $\mathbf{h}$ is an $N$-column vector, $\mathbf{W}^\top$ is an $N\times V$-matrix, $\mathbf{x}$ is the $V$-column vector of zeroes and ones that has a one only at its $k$-th element. What does this mean about the order of operations in $\mathbf{W}^\top_{(k,\,.\,)}\,?$
(Posting comment answers as community wiki)
There are no conventions (widespread operator (sub/sup)script precedence rules) that serve to disambiguate such expressions. $\ \ $
– Bill Dubuque Jun 21 '24 at 20:15