They usually are. It’s a process akin to archaeology where they have to carefully wash away the dirt from the root system, measuring as they go. The problem with this method is that it's hard to reconstruct the entire 3d structure of bigger plants like trees so a lot of the root drawings on the site don’t accurately show how deep they go. It’s much easier with small plants where the researcher can control the soil used.
Modern methods like xray CT or ground penetrating radar can do it nondestructively in the field but they’re usually expensive to set up compared to just sending some grad students to dig.
> you'd get an accurate image of a very distorted root system
At the very least, you've taken a 3D system and reduced it to 2D. Additionally, you're exposing not only the root system but the entire microbiome around them to light and, almost certainly, unless you were incredibly meticulous about sealing, oxygen.
Modern methods like xray CT or ground penetrating radar can do it nondestructively in the field but they’re usually expensive to set up compared to just sending some grad students to dig.