Not surprising considering that
the leaked GBA emulator (aka "Sloop", the one GBA NSO uses right now) for the Nintendo Switch has an AGS Aging ROM and several open-source accuracy test ROMs in the package to test the accuracy of the emulator - pretty telling that the devs were aiming for emulation accuracy beforehand as the NSO GBA emulator passes every test in the AGS Aging ROM.
The first GBA model (AGB-001) doesn't have a backlight, resulting in washed-out colors.
Some games mitigate this problem by increasing the saturation of their colors.
It is until the AGS-101 (aka the GBA SP backlit LCD model in 2005) and later models (excluding the OG NDS since it uses frontlitLCD like the AGS-001), also most aftermarket GBA backlight LCDs have a better color range that isn't washed out than the AGB-001, making some early GBA games look "oversaturated" or "off" like the SNES->GBA ports and Golden Sun in my opinion. The filter that GBA NSO uses attempts to desaturate the colors to resemble the ABG-001's LCD color range.
This is a video that explains it better:
Problem is that not every game was specifically designed for the AGB-001 LCD.
There may be possible cases where the game was also developed in a development kit with a backlit LCD even before backlit GBA models exist. For example, Mario & Luigi: Superstar Saga, a game developed in 2003 natively supports the Gameboy Player by automatically adjusting the color range for the TV and rumble for the GameCube controller.
There is even a ROM patch to force the Gameboy Player color range if your emulator doesn't support "Gameboy Player" mode.
This still doesn't justify GBA NSO forcing the "desaturation filter" as it may as well be a subjective matter at the end of the day.
NERD should've made it into a toggleable option instead, just like every GBA emulator.
At the same time, the Wii U GBA VC has a dark filter that cannot be toggled as well IMO.