My guess would be that dog is gone for good. In the past, when it was gone, there would be some plants or a bale of hay in his spot. Well now, there is nothing there. As if they removed his "mount" for good and covered up the hole permanently. Hopefully I am wrong though. I keep expecting to hear the dog barks during the pirate's song, but nothing happens.
If the animals have been removed to repair or maintain them then I dont think we have anything to complain about. Things break or wear out all the time and a lot of the attractions at DL are now older than the guests viewing them! The temporary removal of a couple elements from an attraction is not reason enough to close it. I do wish Disney would repair things in a more timely manner though.
On the other hand, if they are removing some of these elements because they break and then just plan to leave them out because there is so much other detail to see then thats a real problem. The amount of detail in all of the attractions is what makes them so great.
I miss seeing the donkey and the dog in Pirates, I bet many other guest do too.