A unit's formation doesn't have an explicit effect on combat besides how the men are arranged on the battlefield. When we originally implemented the formation system we had grander plans for how they would influence the battle. Unfortunately these ideas never really panned out in Hegemony Gold which is why we're overhauling the formation system significantly in Rome.

I can see why the peltast description might be confusing. When the description says Peltasts 'fight in an open formation' it is supposed to mean that their formations are more widely spaced then those of a hoplite or phalangite. It's not supposed to reference a specific formation like 'Line', 'Column', 'Open', etc.

when a trireme is carrying a unit and gets in combat with another trireme, does the type of unit it is carrying make a difference to the damage boost?

Yes. The unit on board a trireme doesn't affect the impact damage but it will increase the combat damage done after the ships have collided. The game uses a combination of the unit's melee, missile and defense stats multiplied by their size to calculate the bonus to combat. As units have nowhere to run to, morale is not used for this.

does the type of unit affect the trireme's speed penalty

Yes, triremes with larger units on board will go slightly slower. If I recall the math correctly, a trireme with 60 guys on board will go half the speed of an empty trireme.

We're not planning any really major changes to the naval combat in Rome, but you will definitely be building ships to cross the channel as well as fight the Veneti along the northern coast of france.

As far as the design of the ships, I don't know at what point all of those improvements you describe were made, but the ships in Hegemony Rome are going to be a little different from your standard Roman ships. According to Caesar he actually found the Roman ships were at quite a disadvantage to those built by the gauls. Apparently, the Gallic ships were too thick to be breached by a ram, too maneuverable to be boarded and too tall, even with the towers Caesar built on deck, to be targeted easily with missile fire. Initially, Caesar managed to overcome these disadvantages using long bladed hooks that he used to cut the sail ropes of the enemy ships leaving them floundering and easier to board. Later on Caesar actually designed a hybrid Roman/Gallic ship that he used during his second invasion of Britain.

Yes, the Gallic ships had sails and no oars. One author I've read, Philip Freeman, compares their flat bottom profile more to a viking longship and suggests this allowed them to maneuver into areas where the Roman ships would run aground. Their sides also rose higher above the water making it hard for the Romans to try and board the Gallic ships.

When Caesar designed his own ships for his second crossing to Britain he copied the flat bottom of the Gallic ships to make it easier to beach his army.