When hitboxes are shown (f3+b), completely submerged entities will not appear to have a hitbox when no other entities are on screen. If another entity such as a creeper, an item, a projectile, or even another submerged entity is shown on screen, then the entity's hitbox will show (this doesn't apply to yourself in third person in singleplayer).

Make sure your graphics are set to fast or fancy. ** This bug seems to be fixed for fabulous graphics settings.

Steps to reproduce:

1. Set your graphics video settings to fast or fancy
2. Show hitboxes (f3+b)
3. Clear the surrounding area of any entities
4. Place down water: enough to completely submerge the entity
5. Spawn your entity in the water (if it floats you may have to fix it with commands or blocks)

Make sure you are out of water. If the entity is completely underwater, its hitbox will not show. Now summon another entity (place an armor stand for instance). The hitbox becomes completely visible.

Having certain block entities nearby (not necessarily in view) like shulker boxes, chests, enchantment tables, beds, and moving pistons will also allow the hitbox to be rendered.

For partially submerged entities, only certain parts of the hitbox will render.

If you are underwater, the behavior is reversed and entities out of water will have missing hitboxes.