The problem applies if you install the unofficial fixes from Baldurdash - the ones which fix the dialog and tweak the weapons and other minor fixes/bug squashing. The bonus merchants should not affect your game.
I installed both merchants (I have the Collector's Edition, I added in the other bonus merchant later) installed some time ago, way before I had ToB installed. I continued my SoA game and thus far everything is fine.
So in my experience installing the bonus merchants is fine.
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"Butt-kicking for goodness!" - Minsc
"Cities always teem with evil and decay. Let's give it a good shake and SEE WHAT FALLS OUT!!" - Minsc
