Hmm, got out my Soya to look before answering.
That's a unique situation. (The entire superstructure face piece- all decks, full width, is a single clear part.) I would and will do it like an aircraft model- yes, lots of little pieces of tape. I suppose like an aircraft it would look better to tape the whole thing, cut around the windows and pull off the rest. But they ARE small. This'll be a tough one to get right.
Usually I have the windows on ships be gloss black or dark blue. It looks the most realistic to me. In which case I paint them last. I'm not so sure Hasegawa has the best idea here. Also, they want to make your life doubly difficult by masking on the inside too and painting the rest in there "interior green". That wouldn't be as hard because you could afford to be imprecise, since it all will NOT be visible. Personally they I think they had the kit designed over in the aero dept.
To mask all the portholes on the deck level, I hit each one with a little dot of white glue on a toothpick first, but it takes a while to get consistent results.
And all this on a part about 30mm by 20mm.
When kits have holes where the windows go, I use Krystal Kleer tinted dark.
You'll be best IMO painting them black, or dark blue, or really dark green like the sea. It's reflected light after all.