What WD do very well though, is pick cars that are desirable when they are at, or not far from the bottom of their depreciation curve. The series is almost a predictor for cars that will appreciate in value, especially when it's something relatively modern that they do.
Sure, they may not pick the best examples (few episodes talk of number of owners, miles, service history, though occasionally you can catch a glimpse when they flash up an eBay ad or something in the earlier shows), but their point is spot on, and more often than not, the values paid are realistic.
You only have to watch an old episode and see how much they paid for the car and then look at what that car costs now to see this...
Mk1 Mini for less than a grand.
BMW M5 I thnik was 5 or 6k (most over 10 already)
Sierra Cosworth
Any Porsche they have done.
Etc.
As for hidden work and / or deflated prices - they are all like that.
People pop onto the Lotus forums now and again declaring that WD paid X to get Y HP from the engine in the series 2 they did. The problem is, the cost was underestimated (or didn't reflect all the work) and the HP figure exaggerated