With these settings:

    "editor.fontFamily": "Fira Code",
    "editor.fontLigatures": "true",

    "[javascript]": {
      "editor.fontLigatures": "'zero', 'ss02', 'ss03', 'ss04', 'ss05'",
    },

I get this in a javascript file:

So all is good (the red squiggly is just about the experimental decorators support).

But if I add this setting:

"editor.letterSpacing": 0.2,

I've lost the `ss02' set and the triple equals ligature.

And just for completeness here is what I get for just fontLigatures set to true with no stylistic sets included: (as expected)

Should letterSpacing have this effect?

Version: 1.40.0-insider (user setup)
Commit: 515f496
Date: 2019-11-05T14:32:05.211Z
Electron: 6.1.2
Chrome: 76.0.3809.146
Node.js: 12.4.0
V8: 7.6.303.31-electron.0
OS: Windows_NT x64 10.0.19013

Does this issue occur when all extensions are disabled?: Yes