… don’t work permanently.
If you setup a traderoute (eg. from own market to neutral) with waypoint(s) with shift-click, the waypoint is used only once initially by each trader. Thereafter free routes are used.
That means you can never setup a “safe way” to avoid enemy contact.
The normal should be, if you setup waypoints between markets/tradepoints with shift-click, these should be respected anyways, also by new spawned traders or possible waypoint changes.