Is there any reason to use the early siege units?

As you have noted, the main difference between the "seige" units (Catapult, Trebuchet, Cannon) and other ranged units (Composite Bowmen, Crossbows), is that the seige units have a bonus against cities.

However, it is not a small amount - each of them has:

Bonus vs Cities (200)

As such, your table against cities will look like this:

Unit             MS RS
Composite bowman 7  11
Catapult         7  24

Crossbowman      13 18
Trebuchet        12 42

Cannon           14 60

Whether you value this benefit enough to warrant their deployment, compared with the more mobile and higher base-damage units such as Composite Bowmen - is entirely up to your strategy.

However, the Bonus Vs. City is the main advantage of these units, and should be considered the main differentiating factor between them and the other ranged units.

As you said, they get a bonus when attacking cities. This is not a small bonus- it's a 200% increase. That's 24 strength for the catapult (vs 11) and 42 (vs 18) for the trebuchet. When you're dealing with the high strength, health, and regeneration of fortified cities, you'll need that strength.

Another incentive to use siege units early is to increase their level to get the Range promotion (+1 range) as early as possible.

Early cities are realatively weak and need a few rounds to destroy a siege unit. You can attack a city, retreat, heal, attack again, etc. Later cities, in combination with occupying units, can obliterate a siege unit in one round, so this "training" is not possible anymore. If you have trained 2-3 siege units early on and keep them alive you can siege a city without it being able to shoot back. It's almost too easy from this point on. Even more so, if you also choose Logistics (1 additional attack per turn).

In summary, you build them early to use weak enemy cities or city-states to train elite siege units for later.