This came up in a game I was GMing - I came up with the same two options you did. I ruled it that, if the stellifera were wielding weapons/gear in its hydrobody limbs, then the hydrobody would lose a limb, suffering usual penalties until a new body was reformed as normal (Standard action to dismiss the 'wounded' hydrobody, full action to reform a new 'un-wounded' one.) Otherwise, if the stellifera were wielding items/weapons in its Diminutive body, then that's the body that would suffer the wound penalties, using the general guidance from AA1 that, since it's not stated otherwise, the stellifera body has two arms, two legs, etc. Cinematically, it'd be like losing a handful of tentacles, I reckon. Poor lil' squidly :(
If neither the hydrobody nor actual stellifera body was wielding stuff, I'd leave it up to the player to choose which 'body' suffers the wound: hydrobody, or stellifera body.
In my case, the player chose to take the wound on the hydrobody, and then spent a couple rounds getting back in the fight.