IANAMariner, but I'm assuming the sextant would already be invented, since it would also be important for determining latitudes.
The goal is to figure out when the sun is as-close-as-possible to the reference vector "straight up". On land, we might determine that vector using gravity and a plumb-bob, which is indeed going to be a lot harder on a rolling ship.
However way out at sea, a new option exists: The horizon is no longer an arbitrary mishmash of mountains and hills, but instead self-leveling water in every direction [0], meaning you can safely assume "straight up" is 90 degrees [1] from all points on the horizon.
So you'd measure the angle between the sun and the nearest horizon, and then noon would be when that angle hits its minimum.
[0] Tides exist, but I assume they aren't likely to cause one direction to be significantly higher than the other.
[1] Unless you're measuring from very high up above sea-level, but if the civilization can make ships that big then you probably don't need much navigational help.
The goal is to figure out when the sun is as-close-as-possible to the reference vector "straight up". On land, we might determine that vector using gravity and a plumb-bob, which is indeed going to be a lot harder on a rolling ship.
However way out at sea, a new option exists: The horizon is no longer an arbitrary mishmash of mountains and hills, but instead self-leveling water in every direction [0], meaning you can safely assume "straight up" is 90 degrees [1] from all points on the horizon.
So you'd measure the angle between the sun and the nearest horizon, and then noon would be when that angle hits its minimum.
[0] Tides exist, but I assume they aren't likely to cause one direction to be significantly higher than the other.
[1] Unless you're measuring from very high up above sea-level, but if the civilization can make ships that big then you probably don't need much navigational help.