This depends on what you mean by "skipping" waypoints. In Experimental, a convoy will always compute the full route from one stop to the next, and not simply stop at the next waypoint (this is important for railway signalling to work properly). What it will do is calculate the route from the current location to the next entry on the schedule, and, if the next entry is a waypoint, calculate the route on from that point to the next entry and so on until it reaches either a stop or the same place as it started. Waypoints are thus still effective, but, unless the waypoint is a reversing waypoint (marked with an [R]), which are treated differently, and which do not apply to ships, the next destination shown in a convoy's schedule will not actually be a waypoint, but a stop.