Yes, all of these things make a difference, even the bridge pins.
The opinions on nuts and saddles have been covered in the previous posts, and I have nothing to add.
Bridge pins have an effect because they have weight, and that weight is part of the bridge. Changing the material of the bridge pins is only significant if the weight of the pins changes. Adding(or removing) weight to the bridge will affect the main top resonance frequency.
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Rodger Knox, PE
1917 Martin 0-28
1956 Gibson J-50
et al
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