question

I don't know how you got to using connections[], but it is just a shortcut to access the node where the port connections of an object are stored in its attribute tree. So using this here will naturally not do anything/produce errors.

Your logic makes sense if you add the created points to an array and use those entries in contextdragconnection().

Table points = Table("Locations");
Array GISPoints = [];
Model.find("GISNavigator").subnodes.clear();
for (int i = 1; i <= points.numRows; i++) {
    string id = points [i][1];
    double lat = points[i][2];
    double long = points[i][3];
    Object point = Object.create("GIS::Point");
    point.setProperty("Latitude", lat);
    point.setProperty("Longitude", long);
    setname(point, id);
    GISPoints.push(point);
}

Table routes = Table ("Connections");
for (int i = 1; i <= routes.numRows; i++ ) {
    for (int j = i+1; j <= routes.numCols; j++ ) {
        if    (routes[i][j] == 1 ) {
        contextdragconnection (GISPoints[i], GISPoints[j], "A");
        }
    }
}

Furthermore, I would suggest to format your table differently, otherwise you will have to take into account an offset in the index between the locations and connections table.

Additionally your code currently only looks at the upper right half of the table (which makes sense if the table were symmetric).