Do some still drill out their portholes?
Just started building the Trumpeter Z-30 destroyer and I keep on looking at the portholes and asking myself should I or not or just paint them black?
If I were you I would paint them black.
Forward gun turret of Z-39 in Boston harbour (post war) showing some of the portholes.
Nothing to see except a black circle.
I think some navies/ships had porthole covers, hinged on the outside, to close the porthole for blackout and combat operations (“all” close-up photos are daytime and non-combat …)
The photo of Z-39 does not show any external covers so I presume they were on the inside. Makes more sense from a handling point of view…
General idea (this one is from late 19th century):
If the solid cover is closed on the inside the glass would still make the porthole appear as a dark circle seen from any distance (very very dark grey instead of black ??).
If the portholes are drilled out the plastic of the hull needs to be thinned down a LOT to prevent the portholes from looking like deep wells (10 mm ships plating divided by 350 …) or the drilled holes need to be filled with some rod (clear or painted) or just paint.
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Appreciate your comments Robin.
Having not built a model ship since the late 90’s it’s like starting over building these model ships.
I spent far too long on model Armour 
Yes I’ll just paint them or even apply a dark wash after painting.
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Would agree with a dark wash. I’ve drilled in the past (seemed like a good idea at the time) and the problem is not only looking a little unrealistic, if you go off centre by one or two, you end up with a wonky line of portholes! Fortunately those mistakes were made on ancient Matchbox and Airfix ships, rather than a newer and more costly project.
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Good point Stephen, I’m not the best at doing straight lines as I once nearly ruined a pair of Rock shox mountain bike forks worth £400 trying to cut down the steerer tube with a hacksaw 
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