I have read that the £100, to be given in respect of Council Tax announced in the budget, is to be paid along with Winter Fuel Payments.
Am I missing the point or does this mean that those people who do not pay because they are in receipt of full CTB will still get the money?

yeah think that's right - see the Bill @ Extra money for pensioner households: Age-Related Payments Bill introduced in the Commons for details re eligibility

plus update from yesterday's news story £100 payment for people aged 70 or over: Government confirm claim deadline

It sure is right...

The government has no way of knowing which person is receiving 'maximum' Council Tax Benefit. This is because there are something like 402 (approximately) local authority's paying Council Tax Benefit. The entitlement calculated by those local authority's is held on individual computer systems, and there are many different computer packages available to local authority's, made by different companies, and they are not even compatible with each other, let alone the government's computer systems...

Like HB, CTB is not tied into the main social security computer systems, and so the government can never accurately know what amounts are being paid on any individual case, (you may have seen posts on other topics about 'data matching', this is where LA computer systems are cross-checked with the DWP's etc. systems, but a substantial amount of the 'discrepancies' that are thrown up by data matching are just admin delays, not errors, though these facts are seldom released in the public domain).

Besides which, if the government even attempted data matching pensioners to the £100.00, it would take many many weeks (months) to complete, during which time, pensioners would have become entitled to, and others would have lost entitlement to, maximum benefit, so you would then need a small army to administer and look into those cases...