I would suggest to leave breakline ends separate at a junction. RiverGIS filter out mesh points located to close to each other, so if your breaklines are connected you will loose some points. The threshold distance for nearby points is 0.75 * cell size.
Consider you cell size and breaklines attributes: cellSizeAcross and number of rows - this will give you an estimate what should be your breaklines endpoints distance if you want to keep all of the points created by RiverGIS.