If chaplains are there to give secular "advice" they don't need to be chaplains. They can be Youth Workers or something, if we assume that there is a level of giving advice to young people that falls short of "counselling"; so to talk about making sure that they are qualified as Youth Workers misses the point. People who are qualified in that way need not be ministers of religion or anything similar.
No matter how you cut it, even if there is a role for this kind of youth work in schools (which there may be for all I know), there is no reason for it to be performed by "chaplains". The government has got to stop trying to have this both ways.