Price, for one. True species tend to be a bit more expensive than the hobby form. As for telling them apart, it's usually the coloration. With B. albopilosum, the hobby form has a tan body with blonde setae and the Nicaraguan has a black body with blonde setae. With B. vagans, the hobby form has a cream colored carapace and the true form is pitch black.
Because the true forms are often difficult to get. The Nicaraguan B. albopilosum was next to impossible to find when I first got into the hobby, and now you can pick them up for $50. Times change. It's not that we're okay with it - I'd bet the majority of people would prefer a true species over the hobby form. It's that you often don't have a choice.
Wow, I am kind of sad hearing this but not all that surprised, I am pretty green when it comes to T's but I know how bad inbreeding can be to a hobby like this from years of breeding Cichlids.
It's even more common with cichlids because most people keep mixed tanks. It's actually very difficult to avoid because all-male tanks often result in lots of deaths. And not many people are willing to keep species-specific tanks. At least with Ts, each one must be housed individually, and the keeper makes a conscious decision to pair them. No accidental breeding should occur with Ts.