In general flash cart/emulator/gba hardware fans terminology the logo is only seen after a hard reset, while the lack of one is from a soft reset. http://problemkaputt.de/gbatek.htm#biosresetfunctions
has some more for the technically curious.
Soft reset has some issues but also some perks for some types of hack*, indeed for much the same reason. Different flash carts can do things to try to improve their odds of not having issues with soft reset and may indeed vary with what is the default approach between versions. Users tend to like soft reset as it is quicker to boot as well. Also yeah unlike certain hacks on various other systems there is no way to bypass the GBA logo that anybody has ever discovered (see autostart on http://problemkaputt.de/gbatek.htm#dscartridgeheader
for one example), much less programmed into a flash cart. The health and safety screen that appeared in some later GBA games needs individual hacks on a per game basis to bypass (unlike the DS where it is doable with a firmware hack), a few such hacks exist but not many and while it is a reasonably easy thing to do if you know the fundamentals of assembly (it is not a stealth loading screen and you are getting the game to bypass something it does rather than do something more) then you still need to know the fundamentals of assembly. https://gbatemp.net/threads/gba-health-warning-screen-removal.79929/#post-1051333
for an example.
*soft reset basically just jumps to the game start and goes from there with whatever is in memory being in memory. If the game fails to clear it then what it thinks should be all 00 or random data (memory tends to be random when first powered/uninitialised) might not be as random as it things (see RNG manipulation), might do things for borders, might do things for injected code or data, if the would be hacker floods the memory with data then whatever is what the hacker flooded with is likely free memory for their own hacks (for the DS but see older versions of DSATM's "DEADBEEF padding" option).
I have not got my omega set up right now so can't do a test but hopefully you know the terms now.