Is there a way to disable ChkTex in a specific directory?

I don't know about the LaTeX-Workshop (I don't use VSCode), so there may be some way to configure it to not run ChkTeX for some files/folders.

There isn't (currently) any way to ignore certain files from in the .chktexrc file. However, depending on how LaTeX-Workshop actually works you might be able to put a .chktexrc in the same directory as the files. If that directory is the working directory of the ChkTeX process spawned by VSCode, then it should pick that up as the last .chktexrc file, and hence the one with ultimate authority.

For a quick way to turn off all warnings, you can set --format to an empty string in the .chktexrc:

CmdLine
{
  --format ""
}

If that doesn't work for you (it's quite possible that VSCode always spawns the process in the same directory but with the full path to the LaTeX file), then please open a ticket. It may also be that you are wanting to suppress warnings for certain files that you include, which would require code changes as well. To give you fair warning, I haven't been great at getting to open tickets lately because I've been busy with other things, but at least that way it won't get lost.

You can also use file suppressions if the number of files and warnings is small and the files are under your control (though I'm guessing that's not the case). To suppress, for example, warning 12 in the entire file just add a line to the beginning of the file like

% chktex-file 12