The reason why you can’t find anything in the HB Regs about illegal immigrant partners is that the Regs don’t say anything about it. These are normal couple claims in every respect including, as jmembery says, the NINO requirement. Whether the absence of a NINO for the partner would retrospectively invalidate HB going back over the last two years I don’t know … the requirement arises at the time when a claim is made and if there has not been a new claim during those two years then the NINO requirement will not have arisen (and it won’t again unless and until she has to make a new claim).
The cancellation of IS is not surprising: if she has been claiming as a lone parent, then quite apart from any concerns about income and capital she simply doesn’t meet the threshold conditions for IS. She should instead havev been signing on unemployed for JSA(ib), something she is going to have to start doing now unless the partner’s income is too high. But her IS and JSA problems needn’t concern you directly: if you are satisfied that the couple’s income and capital at all times has been low enough to leave at least some HB entitlement, then you just have to work out how much and calculate whatever overpayment there might have been. If at any time the partner’s income has been high enough to trake the couple out of HB entitlement, a new claim is required and the NINO problem will bite.