Yeah, I can't lie... It's very frustrating when I just pass through an opponent in the air with my jaws wide open. My man needs a hitbox as big as his appetite.
For swallowing bombs, I wish it would work on mortars and landmines, but alas... It only works on 3 attacks, the 2 Links' bombs and Snake's grenades. I guess Peach's bob-ombs once in a blue moon. It really only works against the Links since Snake's grenades explode really quickly and the grenades are tiny. With Link however, the bombs travel slower and are larger, so they're easier to catch.
To effectively use them, you'll want to catch them with an airdodge or whatever. Then jump into Link, z-drop the bomb and immediately eat it. However, this is super easy to avoid. If you want to combo into it, you'll need to catch a bomb, land a bite asap, bite throw into full jump, bomb drop, bomb eat. The other way is to catch a toon link using the bomb jump recovery too close to the stage, as in within your jump reach. Get out there and eat his bomb. You will be invincible during the bomb eat and avoid the inevitable b-up while hitting TL. Many links recover with bomb pull glidetoss up+throw forward. If you can intercept that with a bomb eat, you may be able to catch the link before he can airdodge+clawshot.