The original queue for Nemesis was absolutely enormous, way larger than is necessary these days to cater for it's queues. There used to be another extension which more recently formed part of the queue line for Nemesis Sub Terra and prior to that Dynamo. The part that ran around the vertical loop pit I believe has been disused since the construction of Air, perhaps due to the proximity of the ride?
The abandoned toilets obviously come from an era when the gardens were a bigger part of the average visitors day to the park, there were several walks advertised and also a number of places to get refreshments so it would only be logical for there to be toilet facilities. I would make the assumption that demolishing the toilet block was seen as an unnecessary waste of money when they could simply just leave it disused, it is of course in an area that most visitors to Alton Towers would never visit. Generally the only people who do come across it are deliberately looking for it or are those who like to have a bit of an adventure.