Those bugs are too big to be Gnats or especially aphids.
Root aphid adults (fliers) are smaller then Fungus Gnat fliers.
What you saw in your roots? Hard to say without seeing it!
But, by the sounds of it. Beneficial in my bet.
Root aphids go right to the roots and lock on. Not a traveling larval bug.
So what soil? Is there "woody" piece's in it? A FF product?
Yes? Most likely a beneficial.
Next thing is (kinda hard to explain but,) when you have the root ball pulled from the cup. Smell it. Does it smell like nice rich soil? Your golden!
Or does it have a peppery or sour smell? Fermenting smell means anaerobic and that's bad but, not caused by bugs. Peppery or sour, would tell you, you have a root issue going on... The cause could be many things, including bugs damaging the roots....