Who's ever seen a currency where the threepence is much bigger than the sixpence, even though they're made of the same copper-nickel metal? And the 1 shilling is barely bigger than the threepence.
I bet it's patterned after the prewar UK sizes. 3 pence was brass, 22 mm from 1937-48 6 pence was 0.500 silver, 19 mm from 1937-46 Ghana has different diameters, but had a similar size drop even though they were never silver post independence. Kind of similar to how the US dime is smaller than a nickel even though they are both non-silver these days.
These are good points. I was thinking about how the silver coins are usually proportional to their value.
Look no farther than the USA to see an anomaly with coinage. The reason the larger denomination coin is smaller is because originally it was silver while the smaller denomination coin was a base metal. As @The Eidolon notes the dime is smaller than the nickel, but being that they are both base metal cupro-nickel the nickel actually has more metal value now. BTW @Hiddendragon I really like those Ghanian coins. Ghana has been an independent nation for almost 65 years and is one of the few countries in that part of the world with a stable electoral democracy.