I might suggest using a simple RigidBody node on a separate physics layer, that way you can move it and take advantage of continuous collision detection (CCD) for fast moving bullets. As long as the RigidBody is on a separate layer from the other physics, it shouldn't be detected by other nodes in the game.
Or, depending on how your game is setup, you might be able to replace the Area2D with a Raycast2D, where the length of the raycast is the speed the bullet will move at, and the direction it points is the direction the bullet is going towards. The only issue with using a Raycast2D is that you lose the width of aspect of the bullet, but depending on your game and the size of the bullets, it might not be noticeable. Additionally, you could use multiple Raycasts2D nodes with a short distance to get the 'width' of the bullet.
The issue it sounds like the Area2D is having is collision tunneling, which is sadly an issue with almost every physics engine. Without it, performance suffers, but it can be problematic for fast moving projectiles.