Hi @IreneSwift
I just jumped into game to check this and I was able to place a houseboat from the library in edit town with no issues at all. I just clicked on the promising port icon and my game created the houseboat base and placed my houseboat on the base/port/lot. I have not used any cheats doing this either. Next I tried bulldozing a houseboat from another port lot that already had a houseboat and base situated on it and it left the houseboat base behind after I bulldozed the houseboat. Before i could add another houseboat from the library to this lot I had to bulldoze the houseboat base as well so I think it sounds like you are trying to place a houseboat on a base that's already been left behind or you have created somehow which the game does not allow.
Try adding a houseboat to a lot without a base and it should do it automatically for you from the library regardless the size of the houseboat. I have done this 4 times now to make sure it is working properly and it has worked every-time.
I hope you can understand my tests and you can get it to work for you as well :) Don't worry about bulldozing the port when you are bulldozing a port lot I am pretty sure you have to use the port unlock cheat to delete the actual port itself and none of my bulldozing has effected the ports at all.