I've had a 16 sheep pen for about 500 days. I was off-chunk (working on a canal) and when I came back, there were two missing fence pieces. I lost only 5 sheep, but it was weird. No creeper hole, and nobody to trigger a creeper anyway. The wiki doesn't list fence as an Enderman block.
I guess it could have been lightning. I like that theory better than random data loss. I can't be positive it happened in an unloaded chunk. I probably didn't visit the sheep for a couple of days before leaving. (Although it was irksome to be gone 2 weeks and my sugar didn't grow )
The server is on the net, but I would think if someone hacked two firewalls to get to it, I'd have bigger problems than two missing non-adjacent pieces of Minecraft fence.