As far as finding the queen, it would be difficult without modifying the hive to some degree. I think you would need to do at least partial frames to be able to pull them out without damaging the comb. In David Heaf's book "The Bee-friendly Beekeeper" page 121-122 he talks about removing the comb for inspections and also references some modifications that can make this easier. David has put a lot of time and effort into using Warre Hives and much of what he has learned is available on the web. He sites Bill Wood as recording less than 1/2 teaspoon of honey being spilled when pulling to full bars of comb. That would indicate that you can remove comb with minimal damage and do inspections. My experience has been that removing the comb causes more damage then what David sites in his book.
You are correct is stating that the main philosphy behind Warres is not disturb the bees for fear of not maintaining hive heat and scent. I am not one that is going to tell you that it's not a Warre unless you never open it up. I am not sure that a Warre Hive is the best hive for queen breeding. I would think that the Langstoth would allow for easier inspection, removal etc as needed when breeding queens. You can always try it and let us know how it works!
You can find the queen in a Warre Hive by using Warre's methods explained on page 14, 106 in "Beekeeping for All". I have not gone looking for the queens in my Warre hives but just look for pollen being brought into the hive and the bees acting normally. So yes, you can find her but it's not as easy as with a langstroth. For those reasons I would think it easier to use a langstroth for raising queens.