Get him to confirm his code and deductions as (from HMRC website... "If you haven't registered for CIS or the contractor couldn't verify you, they'll have to make deductions at the higher rate of 30%. You can claim credit for these deductions through your annual tax return") until he gets that code then you have to deduct the 30%.
If there is a delay in getting it then dont worry about it too much and just either submit early and tell the 30% guy to sort his own refund out (or get him to pay you to do it ;) lol) or wait, get fined £100, and then write a letter of appeal, they will normally overturn the first few fines if you write a nice letter explaining the issues you've had... I've had three overturned now! :D lol
Have the subbies got their own bookkeepers? If not offer them your services (3 clients for the price of one! you lucky person (get them to pay for it of course!). lol) as they will be able to claim the CIS back (provided they dont go over the tax threshold by much)
Do you know how CIS works? In a tax sense?