Not sure what the labor rate is where you are, but they're likely losing money at $24 for an emissions test.
I'd guess that fee is set by the State ?
I don't know how "abnormal amount of copper in brake lines" would be checked/found, but it sounds like they were hoping to make a few bucks or at least break even.
Kinda like those $19.95 lube/oil/filter deals, the shops are hoping to upsell on any issues they see.
I'd sure want to know what that thumping sound is all about.