1. Presumably you know which deposit scheme was used. Look their details up on the internet. I think you will find that if the deposit is withdrawn from the scheme they automatically inform the tenant. In any case, contact them and ask for information about what happened, why the deposit was withdrawn by the agency (i.e. why did the scheme tnink the agent had authority to do this) & who they notified when this happened. If they did not follow the correct procedure it may be that you could pursue a claim against them.
2. I'm not sure whether the legal advice the tenants have had is correct. It may depend on the exact terms of the tenancy agreement and of your contract with the agency.
3. However, assuming you have to reimburse the tenants (& you must make sure there are no grounds for retaining any part of the deposit before doing so - you clearly cannot rely on the agent to do a proper check out inventory) then your only recourse (apart from the possibility in 1 above) would seem to be to make a civil claim against the agent. However, this will cost you a Court fee & - if they are insolvent - will not produce your money. Theft & fraud is, of course, criminal but I'm not sure the police would see it as such - they would very likely tell you to deal with it as a civil matter. However, you could ask them.