Are you thinking of putting Terrain damage on water tiles? Coast = -1. Deep coast -2, Sea -3, Deep sea -4 etc.
Then you have to add the promotions to overcome them.
Not exactly. You'd have a damage range for a failure to succeed on a Seamanship check on the terrain (probably also greatly enhanced by features). The seamanship check would take place at the initiation of a unit's turn, which takes place at the beginning of the player's turn. You'd also have a threat multiplier. The seamanship rating would be your base rating for avoiding taking damage on the open ocean (which would have a 1 for the risk factor (the lower the worse)) Then you'd have a 5 risk factor for seas (5 seamanship for a raft*5=25% chance of avoiding damage this round) and then maybe a 15 risk factor for coasts (75% chance of not taking damage every round while on the coast) and a 19 risk factor for lakes (95% chance of not taking damage every round while on a lake). The damage on a coast could very likely be fairly insignificant unless you're already on a reef or something. This would give you plenty of time to moor, which would freeze movement but increase the risk factor (thus decreasing the risk) by a lot and thus give the unit a chance to recover, even if very slowly, or get back to a city.
As you upgrade your ships they get better and better seaworthiness (but there should be a minimum of 1% chance for taking damage I think because surprising weather can catch even ships in port and destroy them.) but seaworthiness should also reduce the amount of damage that is taken when the ship does take damage as well. So that raft would reduce the end damage check by 5 as well.
The range of damage for coasts and lakes should be 10-100, Sea 20-200 and Ocean 30-300 (depth is not an important measurement for the danger of overseas travel.) Bear in mind that 100 HP is what nearly all units have as a base (though there are some promos that allow the unit to increase that... a LITTLE... and then merged/higher quality units can have quite a bit more.)
Then ships can get promos to increase their seaworthiness as well. By modern era, it should be very unusual to take damage at sea and when you do you are able to keep it to a minimum or not at all.
Weather Techs could add to the Seaworthiness of all ships, or rather open up equipment upgrades that do that for nearly any ship that gets the equipment (if it can.) This is because it allows the captain to avoid or minimize the impact of inclement weather.
All this would perhaps get some interaction with storms but I'd be initially designing it for the games that don't have storms at all, assuming that storms take place and are gone too quickly to be really SHOWN on the map.