The annual return form clearly states that employment costs should include all costs, including National Insurance, pension contributions, etc. I would think that an office maintenance allowance might not count as an employment cost but an administrative expense.
If the clerk is over retirement age, then they are exempt from employee NI contributions, but employer NI contributions are still payable.
Access to council documents by councillors is a common law right, and would certainly include the annual accounts. Most councils make their accounts public.
Apart from the councillor rights, the public have the right of inspection during a set period of 20 working days as described here: "Each year the Council's Annual Return is audited by an auditor appointed by the Audit Commission. Any person interested has the right to inspect and make copies of the accounts to be audited and all books, deeds, contracts, bills, vouchers and receipts relating to them". (The new audit arrangements are a bit different, but the same principle still applies). So accounting records cannot be kept secret.
Personally, I'd be disinclined to worry too much about mistakes in past returns provided the problem is only that the costs have been recorded in the wrong way but the overall figures are correct. However, it is certainly a good thing to make sure that future returns are prepared correctly.