The tool I recommend is a [dwarven atom smasher][1].

First, you designate a 1x1 [dumping zone][2]

Second, and not necessarily in this order, you build a drawbridge that slams down on said tile.

Upon smashing down the drawbridge onto the tile, you obliterate anything smaller than an elephant (all items and any creature up to a zie of 1200000cm³). This can remove excess items, pets, population, invaders and consequently improve performance.

Note: If items end up being dumped onto an open drawbridge, raising the drawbridge will instead launch the items (and dwarves) in whatever direction the bridge closed.

EDIT: To answer the "useless seeds" bit:
I copy-pasted the source seed into excel and filtered by your criteria. All of the resulting seeds are tree seeds, i.e. abaca, apple, apricot, avocado, banana and so on. Trees grow on their own and there's no tree planting functionality in the game. To answer your question, you are right in that the seeds that match your criteria serve no purpose and can be smashed.

  [1]: https://dwarffortresswiki.org/index.php/DF2014:Dwarven_atom_smasher
  [2]: https://dwarffortresswiki.org/index.php/Garbage_dump