I have noticed that these chariots are not present in any lists? i.e 3-man 2 horse chariots with bow and short spear. They usually appear as a contingent/ally in the Syro-Canaanite army. Have I missed them somewhere?
Ugarit is covered by the Syro-Canaanite list, their chariotry is considered functionally identical to other maryannu chariotry.
Should they not take account of the 3rd man with javelin as 'melee expert' in a similar way as the Hittite Empire 3 man chariots?
Well, IMO the Hittite ones shouldn't get the ME anyway ;D
Must confess I am unsure about the evidence for the Ugaritic chariotry so can't really comment - what is the actual evidence? I have a recollection of seeing something that suggested that any 3rd man was a "groom" and the 3rd horse a spare. This probably - https://www.jstor.org/stable/543092?read-now=1&refreqid=excelsior%3A0ca191007972e7085690f2f7fca16727&seq=1
The idea that Ugarit used a third crew on the chariot seems to be based on the idea that they copied the Hittiites. It appeared in the WRG lists and has been a "wargaming myth" ever since. However there is no evidence for this in any primary source that I am aware of.
Indeed the only evidence for a third crew member in Hittite chariots is in the Egyptian account of the Battle of Kadesh and this appears to only be mentioned because it was so unusual. The theory I think is most credible is that the third crew member wasn't a usual crew member but was an infantryman carried along to support the attack on the Egyptian camp. The Hittite chariot training manuals that have survived (and have been used by race horse trainers even today) make no mention of a 3 man crew.
An Ugaritic source does mention each groom is responsible for 3 horses and this did get interpreted as the chariots being 3-horse chariots. It seems likely that the third horse was a spare. Another possibility (as some later carvings do appear to show 3-horse chariots), is that the third horse wasn't yoked to the chariot but was used as a shield to protect the 2-horses that were yoked to the chariot. As the chariot wheeled away the horse would be on the outside. If it got wounded, it could be let go and the chariot continue with 2 horses.
I have considered a special list rule that instead of giving Hittite chariots melee expert, that they should be capable of attacking fortified camps without dismounting (but as if dismounted)!
Richard