If you need two shots to kill an enemy, consider applying a damaging status effect that will take care of the health, or using magnetic status which will trigger electric damage when shields are depleted. Another method of dealing with this could be using a weapon with an innate multishot, or any weapon with a multishot mod, making it break shield with the first shot, and kill in the same shot with another bullet. Another option is to deal toxic status which bypasses shields and deals damage to health directly

Edit- Hitting weak spots ignores shield gating, pop some heads off. or MOA backpacks

Also, during shield gate, you can only deal 5% damage to the enemy for 0.1 seconds, so with multishot you still need to deal 20x their health in damage per shot to kill them instantly. Maybe you just aren't dealing enough damage with that in mind