In the past the setting
"editor.scrollbar.vertical": "hidden"
would give an Unknown configuration setting
warning in settings.json and be grayed out. But it would nevertheless work after a reload.
As of v1.58 it appears that
editor.scrollbar.vertical - 'auto' | 'visible' | 'hidden'
editor.scrollbar.horizontal - 'auto' | 'visible' | 'hidden'
editor.scrollbar.verticalScrollbarSize - number
editor.scrollbar.horizontalScrollbarSize - number
editor.scrollbar.scrollByPage - boolean
are all being made "first-class citizens/settings` and will work without a reload or error message.
See Expose editor scrollbar options and react to them being updated.
From the Insiders Build now:

Previous answer:
Probably the best you can do is make them transparent:
"workbench.colorCustomizations": {
"scrollbarSlider.background":"#9aa0",
"scrollbarSlider.activeBackground": "#f000",
"scrollbarSlider.hoverBackground": "#ff00"
}
There are a couple more scrollbar color properties.