Alas, using the same dice for hitlocs has some advantages, but it does not suit BRP well. You must live with it.
3d6 is nonlinear (it is a bell curve). It is perfect for determining chances of success, as it naturally models casuality and statistics. It is less perfect when you have to design your own critters from scratch.
After designing hit location tables for weird monsters for years for RQ3, I can definitely state that 3d6 is a no-no unless you know that nothink non-humanoid is coming into play, and d100 is definitely more realistic, but a tidbit complicate. D20 is simple enough to design new creatures in a few minutes, and flexible enough to provide for a minimum of realism.
That said, MRQ location table is d20 but sucks. Too linear. (This I say to become a little more popular, as I usually advocate MRQ here ).