Hi jmetz,
I would not recommend removing any standard indexes within the Dynamics SL application database. The soplan table contains the planning records that are created by Process Manager so it would be expected to have a large number of writes to the table. The soshiplot table contains the warehouse / lot serial information related to lines on a Shipper. Again there could be a large number of writes to that table when Process Manager creates the Shippers. Is there any particular reason that you were looking at removing these indexes?