If you do not modify the base scripts, events and anything related to the base rom, and only keep on adding your own scripts and events onto that same rom, then those scripts stay there occupying space.
If you wanted to delete a map of Pallet Town in Advance map lets say, then the map would be gone, but the scripts that were given to those NPC's stay in the rom. But since you cannot "delete" a map in Advance map, you could delete all person events and the compiled scripts would still be taking up the game's space.
But in all honesty, free space shouldn't be a problem for a casual rom hacker as you could use up all existing maps without adding a new one and make a new region without a problem as well as adding text, trainer battles, graphics in the free space that's available in the base rom.
It is usually a good idea to leave the scripts that came with the game intact, as deleting something or altering an existing script could potentially cause problems later on in your rom hack.
