It could still be due to certain nutrient deficiencies... different plants require different nutrients at varying amounts (they grow and uptake nutrients at different rates too), so one type of plant may show symptoms of nutrient deficiency while others are still okay.
When you remove deteriorating plants and the remaining ones recover, it could also mean you just reduced the plant mass, so there is less competition for nutrients and more of it available to the remaining plants, hence they resume growing well.
Have you looked at gradually increasing the fertilizer dosing amounts as the plant density increase? More plant mass = more nutrient requirements, so the fertilizer dosing also has to increase to match it.
As for pin-holes on leaves in general, its usually linked to potassium deficiency, so maybe try increasing K dosing to boost up those nutrient levels, see if that helps.
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