S1 & S2 are low-body. S3 are high-body. Very simple.

If you look at 224, it sits, well, low, hence the moniker low-body.

Here below is a brief synopsis from the ILR:

There are three distinct Countach LP400S Series.

Series One - The first 50 cars delivered with Campagnolo "Bravo" wheels in 1978 & 79. The very early 1978 cars had the original LP400 steering wheel. Small Stewart Warner gauges, 45mm carburetors and a lowered suspension (low-body) setting is a trademark feature of this celebrated first series. Halfway through 1979's production, bigger gauges were employed. 50 cars were built and the last one is noted to be 1121100*

Series Two - These cars are recognized by their smooth finish dished/concave wheels, and still retain the low-body setting. 105 cars were built and the last one is noted to be 1121310*.

Series Three - It is claimed that from chassis number 1121312 onwards, the cockpit space available was raised by 3cm. These cars are recognized by their raised suspension setting. 82 cars were built, and the last one is noted to be 1121468* They have the smaller 42 mm carbs and are noted as the slowest of all Countach variants.