Yes, it's an advantage to play with 6 members.
Each manager has a max of 48 possible points they can achieve per season. So if an associations play with less than 6 members they are leaving points on the table.
That said, if a manager is only picking up like 12/48 points per season and a suitable replacement cannot be found, it's probably best to play with less than 6 until an adequate 6th member can be recruited.