Well, we do know that there would be night and day, and there should be enough variation for the two to be separate maps.
You would probably want to start with the day map (since it'd be more colourful), then when it's pretty much done, you derive the night map by darkening it or palette swapping the brightest colours. Then of course you change the things for the night...closing up flowers, changing other plant life, raising the tide level, closing up buildings, opening/closing certain dungeons (though most of that should be taken care of with the specific day/night obstacles). I was hesitant to have the water frozen during the night as that sounds too much like Oracle Of Seasons, but I suppose in the vicinity of the icy dungeon there could be a couple small patches that become ice. You could have a large animal blocking a path (like the walrus or whatever it was in Link's Awakening that blocked the desert) that's asleep or in a different position. Or a group of people in different positions, like in the excavation area. (The thing about the tide...it's probably easier to show it rising if it was the whole south portion. But I guess you didn't want that. It's still doable on the side, of course, and you'd find a way.)
There's lots you could do, and yet it would still be relatively simple. It doesn't have five "worlds" like Seasons (you mention Subrosia and Holodrum, but Holodrum had four seasons (and you also mapped the "default seasons")), and the two "worlds" wouldn't be as varied as the time periods in Ages. Heck, day/night shouldn't even be as different as the Light/Dark Worlds of A Link To The Past. You're changing some things, some of which are tile replacements (yay for Revned's tile slicer/splicer), and other minor things, but you wouldn't be altering the landscape or structures at all (other than the overall colour).
I actually think it'd be kind of fun...depending on how the time goes I could do the nighttime map instead of a third (or fourth!) dungeon if time allows if you didn't want to do it. It seems like that'd be the most fun part, actually. I've always enjoyed multiple "worlds" in the same physical space. But if you made the day map, I think we'd both want you to do the night map if it's as simple as I'm thinking it will be.