After a long time of trying out what I could do wrong, I come to the conclusion that dims x,1,16* for harbours are not supported, because of three issues:
1) harbours which would stretch out to the north or west will stretch out over the land instead. This only affects placing such harbours, if you place them to the east or south and rotate the map they work.
2) already placed harbour tiles in the ocean will not change graphics when another harbour is placed next to them, while the freshly placed tiles will.
3) if two harbours are placed next to each other, deletion does not work properly. You can sometimes delete only the land-part or only the sea-part of these harbours.
Especially the first one seems like a minor issue, and the second one could be removed by only allowing the land-tiles to connect, not the sea tiles (still much better than using 1,x,4), which might remove the third issue as well.
*it should actually be 1,x,16 since it's 1,x,4 that works - but this results in harbours parallel to the coastline, not even close to the desired result.