It is not nescesery to kill every boss in every district to be able to fight El Sueño. The bare minimum is 8 total boss fights before the big guy. If I finish the game in this way and skip more than half the bosses, would I be able to then go back and fight every one of them or is it if I kill El Sueño it's credits and thanks for playing ?
Yes. After you complete the El Sueño mission, you will receive a prompt saying that you did not 100% complete the game and you will be allowed to go back to complete those other missions. Once you have 100% completed the game (all bosses and all side missions), the other ending will unlock (so play the EL Sueño mission again).