The long standing bug (MC-10176) allowing players to break blocks design to be unbreakable (Obsidian, barrier blocks etc.), aswell as any other blocks in the game has been fixed as of 1.8.2-pre4. This would mean holes will no longer be able to be formed in the nether ceiling once we update to this version, I will therefore begin blocking up all holes in the bedrock after we update to ensure fairness among all players. (I believe it would be unfair to allow some players to continue using/abusing this exploit, whilst others cannot).
I recommend you retrieve any blocks/chests from above the nether as soon as possible, as it may not be possible to do so once the holes have been repaired.
It may be possible to get up there by other means, still. My ruling on no significant structures up there still stands, but you should consider any item up there at risk of a Guardian assuming they are abandoned and destroying them once we update to 1.8.2.
Bug MC-10176: https://bugs.mojang.com/browse/MC-10176