Reduce BOM Lines or reduce BOM cost? How to make production cheaper?
The obvious answer to your question is that it really depends on a number of factors. You have to weigh the cost per part versus the cost per BOM line to determine the most cost effective approach.

On thing that can be said though if you are working on BOM line item minimization is to first concentrate your attention on those lines with the lowest part costs. This will almost assuredly be first in the SMT resistor category followed closely by the low capacitance valued SMT capacitor category. The biggest gains will come here. Think seriously if you have 10K and 12K resistors if you can have both lines be the same value....even if that ends up being that you end up specifying 1% resistors for both line items.