Spending policy amounts for a particular year are stored on the fund summary record for the fund for the year.  Along with the spending policy or cash requirements amount, there are summary values for gift and grant activity.  The manually adjust spending policy tool displays all fund summary records regardless of whether there is a zero on non-zero value in the field.  (After all, if you are going in to add a spending value, you want to see the 0's) .

If there is a missing fund in the tool, just click the add button to create a record to hold your cash requirement amount.

You can't delete them, nor should you really want to since the important piece of information is the spending policy amount, not the existence of the record. When you run the spending policy calculation and then click on create spending policy you might get warning messages about missing fund summary history records.  That would happen if a particular fund did not have gift or grant activity for the year and this is just a notification. At some future time, the warning messages might be removed from the report display.