I agree with the others that it depends on the ship's status (so, check your photographic references!). For me, it's also a question of diminishing returns, in the scale I build, 1/700. They're just too small, and unless I'd build an elaborate jig, it'd be too easy to misalign them.
Also, are you building a ship during a phase of its life, in which its portholes were plated over, to provide more integrity against flooding? Maybe you need to fill molded-on portholes, instead.