How does rated motorcycle ccs work?

Specifically, I noticed that virtually all displacements of motorcycle engines are just slightly underrated. For instance, the Kawasaki Ninja 250 engine is actually 249cc of displacement. Similarly, the Honda website rates the 125cc from engine at 124.9cc. I've noticed this with a majority of motorcycles I've come across; their true displacement is slightly below their rated displacement. Any ideas why? Is this for some legal purpose?

When talking about displacement you always round to the nearest whole number that's just always how they have done it

Some places rate motorcycles by 'above' or 'below' a certain displacement. Like motorcycles 250cc and over pay a higher taxes, or motorcycles 150cc and under are allowed on major roads. I think a lot of places, taxes are based on X no. Ccs and over, so a 249cc engine is under 250cc so it avoids the tax.

It is called rounding off. 250cc looks and sounds better than a 249 cc.

When calculating the volume of a cylinder one uses Pi x radius squared x height, so you will always reach a figure that has several decimals - unless you alter the height and radius to create a whole number so even 124.9 will not be as accurate as you can get (given that Pi can be calculated to thousands of pages).

Partly.
In many places motorcycle tax or licensing is limited by cc.
Being just under the cut off size is legal bring just over is illegal.
Selling the whatever 124.9 sounds silly compared to the whatever 125.
In the UK learners can only ride up to a 125.
A 126 would be no use. A person with a license to ride a 126 is likely to buy a lot bigger bike so no sales.

A Suzuki S40, AKA LS650, is 652cc.
A Vespa LX150 displaces 150.46cc.
A Vespa Primavera 150 is actually 154.8cc
etc.

The stated displacement is "close enough" -- unless the law cares. In the UK 125cc is the learner limit, so the bike has to be a hair under 125cc. In the US, in some States the minimum displacement on the freeway is 150cc, hence the small scooters have a bit more.

Jap bikes are in metrics, whereas AMERICAN bikes are in the STANDARD or cubic inches.

A 2-litre car rarely has a 2 litre engine - it's usually between 1,990cc and 1,999cc.

The same applies to 5-litre cars, or 3-litre cars or any other engine capacity you care to mention. It's just convention, nothing more.

Sometimes in some markets it is simple rounding, no other reason. IN some market there's a very real legal reason for just under a specified legal limit. UK and some other European markets have a 125cc 'break'- under 125cc is legal for younger, newer riders to ride on road, over means need to be older, more experience. In US markets the federal law says 150cc to ride on interstate highway system, under that size is not supposed to be allowed. California and Illinois- possible some others- have Graduated motorcycle licenses that restrict new rider to under 150cc so they are not allowed on interstate system, have different color license plates for the smaller models compared to highway legal models. Minor over the 150cc break means a 151 cc scooter can go on interstate system- Dimo rides one of those barely legal models, I used to ride a 154cc Honda Dream that was legal in Illinois for same reason. 250cc is a secondary break for some states- Ohio used to have that size break and Texas poster notes learners permits have restriction of under 250cc - can't legally ride bigger for awhile, Mandatory insurance by engine size, license plates issue by size may make the just under or over very important issue. A 49cc engine-under 50cc- is limit for 'Moped' license scooters with speed restriction in Wisconsin--and no motorcycle endorsement needed then

In your example, 250 is the nominal size, just like a 2 by 4, which isn't actually 2 inches thick by 4 inches wide. My 1600 Kawasaki Vulcan was in reality 1594 CC's.