I'm trying to replace the rocket explosion's model (in my opinion models/weaphits/boom01.md3) by a cartoonier one, but no matter what kind of model I try to bring into the game, it still appears the same flat plane or sprite.
I did the same with the bullet explosion (models/weaphits/bullet.md3) and it worked without any problem. - Strange...
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By your mention of .md3, I think you mean Quake 3, and not Quake 1/2?
If thats the case, the explosion isn't an actual model, its an animated sprite. The bullet impact is a model in Q3, so when you replaced it, it would work like you imagine. However to replace the explosion effect in Quake 3, you must edit the textures in "models/weaphits/rlboom/*.*"".
Keep in mind you wont be able to change the model unless you mod it in (I think?) so you will just be working with an animated sprite.