The scale of the kit and the thickness of the plastic are two major considerations.
The 1/350 scale Enterprise kits have windows that average right around 1/4" wide for most areas of the ship, but at 1/1000 scale, those holes become the diameter (roughly) of a #75 drill bit. The plastic is roughly the same thickness, but the differences in how light gets distributed is pretty remarkable. As you get smaller (1/2500, 1/5250, etc.), the holes become smaller still and both keeping the twinkling effect down and drilling straight, even rows of holes become issues.
Those large scale ships measuring out to 1/350 have some tricks to them. Some builders will lightly sand the clear parts the kit supplies to help even out the lighting to prevent the twinkling effect, while others leave them out entirely and wait until after painting the ship to fill the window openings with canopy glue. That gives the appearance of glass, but it is not optically clear, so the light is diffused and scattered evenly.
Some areas of the 1/350 NX-01 are more easily lit with fiber optic simply because of space issues. There just isn't a lot of room inside the kit at points to run a lot of wiring or not enough clearance for light strips to sit and allow parts to come together properly, without gaps. The fiber optic is relatively easy to use in those areas.
It comes down to your preferences and the variables you find in the kit whether to use strips, fiber optics, electro-luminicent sheeting, flo-tubes, or daisy chains of LEDs to get the effects you have in mind.