I've attached a track showing this issue. This was on the latest open beta (2.5.6.57264). I drop three passes of a harrier fully loaded with Mk82 on the 052C and get it to around 33% damage. I try to fly through the ship every time, but only when the damage is greater than 33% can I fly through it. I shortly crash afterwards, but that is because I hit the water.
It appears to be the 'second' damage state where the large holes appear that causes the hit box to go missing. I didn't show it in the track, but if you try to damage the ship further the bombs explode on the water and only splash damage affects the ship, doing ~1% damage every time, down from the 12% it does with a working hitbox.
I haven't tested the other ships, but I have heard of issues with the 052B and C and the 054A. ShipHitbox.trk