One can reproduce with HC theme, but also with any theme which redefines input.border.
In VS Code:

In Theia:

Same for SIW:

Also, no borders around the dialog buttons:

This issue is the same as https://github.com/eclipse-theia/theia/issues/6743, isn't it?
This issue is the same as #6743, isn't it?
It is not about HC. HC is only a way to reproduce. You can create a custom theme with another input.border color and it won't work.
I cannot see what files are selected in the explorer either.

I cannot see what files are selected in the explorer either.
This one I think already about HC support :) Maybe file a new issue just to be sure that does not get lost while fixing this issue.
I am going to look into this and #6743.