I would say that if you aren't comfortable with the advice the trainer gave you, then find another trainer.
My guess is that he suggested a bare crate because if the dog urinates in it, he will have to sit in it. Personally, I don't crate train that way. My experience has been that for a while, some puppies urinate in their crate…eventually they grow out of it. But I am very tolerant for cleaning up puppy pee and poo I do line the crate with newspaper so it absorbs any liquid...but the important part is that a puppy really should be taken outside at most every couple of hours to become housetrained...if you don't or can't do that, it will take longer to house train a dog.
As far as citronella collar for nipping...I don't think it would be effective. I think it is far more effective to disengage with the puppy..it sends and immediate message of "I won't play with you when you put your mouth on me". If it is true puppy mouthing, it will get better as the puppy grows up. If it is some bratty temper tantruming, then if you don't deal with it, it will get worse.
You really need to find a good, positive reinforcement trainer...I think that will help you. Somewhere, maybe this thread? there is a link to the American Pet Dog Trainer website, most of the people listed there are well educated in positive training techniques. For even more certification, look for a trainer with the CPDT (Certified Professional Dog Trainer) title. You can also google CCPDT, and find a listing of these trainers there.