You wouldn't have a claim against the agent as you arent a potential tenant and haven't suffered a loss. Your son may have a claim, however his only loss so far is the reference fee - he hasn't yet paid the deposit. In any event, would your son co-operate with a claim? Would the other students, who just want to move into the house? Are you prepared to pay the court costs yourself for the whole group, as this will be more than the deposit you are disputing.
The agents, like it or not, have ignored you so far and will probably continue to do so.
I think you are worrying unecessarily about failing the referencing - the agents just want the house filled with as little hassle as possible and it is obvious that a six bed house will only go to students who will fail standard referencing. They probably won't bother to reference them at all, PROVIDED they get guarantors on board, however I appreciate that the referencing costs are ridiculous.
Have you really thought about the other five tenants who have been brought into this? If the tenancy doesnt go ahead they may well lose their deposit and even if the agents eventually refund it, there will be a considerable delay and in the meantime they may not be in a position (or their parents/guarantors may be unwilling)to fork out a second deposit on another house.
Do you want your son spending the next academic year living alone because he has lost his friends over this?
BTW, it is perfectly normal, for student properties, to ask for a deposit this far in advance.
I understand you are concerned about the agents,however it is not obvious that the agents are going to run away with your money. Unfortunately, with most agents (and I have been at the receiving end) it is a case of take it or leave it, and you face the prospect of your son and his friends going through the same situation all over again if this house falls through.
Have the other guarantors been informed of the current state of events?
Dare I say it might be better for all concerned to bite the bullet, sign as guarantor, pay the deposit and hope for the best? It does appear to me that you are digging a deeper and deeper hole for yourself.
(BTW, if this house only has two floors it will not be a licencable HMO).