The Latham & Matthews edition say these “were used in fireships, as combustible material, and for cleaning ships’ bottoms by singeing off the tar (‘breaming’)”. (vol. VII, p.331)
There are two cases when the Diary could have referred to "reeds" in this connection.
The problem seems to be that Pepys' shorthand is open to interpretation, leaving Wheatley and L&M taking different positions.
The first time was on 5 August, 1660, and the discussion starts at
Chart showing the number of references in each month of the diary’s entries.