I tested with 1000 tilemaps created on every tick and apart from a slightly higher memory usage there's no difference in performance.
The funny thing is that you can't actually delete those invisible tiles, even if you erase them, they are still stored in timemap data. The only way to shrink the tilemap is to delete all instances of it, restart the editor, create a small blank layout (say, 300x300 px) and place the tilemap object on it.