There is no such thing as Scene numbering.
The Scene, which is to say those groups bound by self agreed rules*
https://scenerules.org/ (which you can see there were split at one point), often actively oppose numbers as they often then lose the directory names given to the scene releases and with it some information.
*or this if you fancy how it really plays out
The release lister websites like advanscene, no-intro, pocketheaven, abgx, advance-power,
http://offlinelistgba.free.fr/index.php , here and all the rest number things in the order they get released, though they might not always use pre databases. Certain files may not get a number, typically they are non retail releases (games given away in competitions/on magazines, leaked betas, leaked full games that never made retail, demos), sometimes unofficial releases, hardware releases (for the DS one of the first major kerfuffles was the DS browser), if the game is hacked 6 ways to Sunday (for the DS see the Golden Sun releases though some of the stuff with additional binary compression also played, in some cases intros and fixes also saw things get yanked awaiting a "proper" which also annoyed some Scene types) a later release might supersede it. In the case of advanscene these would be the X-files you can see on the side for the GBA and select as an option on the DS.
If you drop one game then everything that follows gets shuffled accordingly.
advanscene also took the questionable route of accepting the "propers" released later in the DS lifetime. Short version there is for many years a part of the DS header was assumed to be blank (mainly because it was) but then the DSi came along with its signing thing (
https://hackmii.com/2010/02/lawsuit-coming-in-3-2-1/ ) and whitelist for the older stuff which used that nice formerly blank section. The Rudolph's dumpers that most used carried on filling in the blanks with blank but in a technical sense that nobody will ever care about (no custom firmware, no flash cart, no emulator, not the ROM itself, only a locked down hypothetical future emulator), and in a practical sense only really serves to frustrate hackers using some of the more modern patch types.