Alright, this seems to be a Cartographer_Mining/Herbalism issue.
_Routes does NOT require _Mining or _Herbalism to run, hence it doesn't check for their existence or whether they are loaded. It does use _Notes though, which it checks for.
When you create a new route, it then checks with _Notes to get the registered DBs and look for _Mining and _Herbalism node data. Once the route is made, the route coordinates are stored within _Routes and it no longer access _Mining or Herbalism again.
When you add/delete a note inside _Mining and _Herbalism, they send a Cartographer event that _Routes responds to to modify routes that involves that zone/nodetype.
Apart from the above, _Routes does not interact with _Herbalism or _Mining.
Please note that _Mining and _Herbalism also requires _Notes to run. If you have _Professions installed, _Mining and _Herbalism will load only if yoour character has the relevant professions unless you override that setting.