The pause marker . . . in the second column is not interpreted as a pause:

%title

# Overview

:::::::::::::: {.columns}
::: {.column width="40%"}

Left column

:::
::: {.column width="60%"}

* First list
    * subitem

. . .

* Second list
    * subitem
::: 
::::::::::::::

The same slide content without the columns markers results in the pause as expected.

Compile with pandoc -t slidy -s test.md -o test.html

Pandoc from ubuntu 20.04:

pandoc 2.5
Compiled with pandoc-types 1.17.5.4, texmath 0.11.2.2, skylighting 0.7.7

I could really use this feature, displaying code in the left column, and content with pauses in the right column describing the code.