roots

I had cloned using a daisy cloner (daisy cloner is fantastic by the way) for my 3 and now the roots are coming out of the bottom of the transplanted clones. I'm using those clay balls as a substrate and dunking them twice daily. They are in their vegetative phase.
The real questions are: will these exposed roots cause me any problems?
will i harm the plant if i trim them down to the outside
base of the container?

personly i wouldnt be cutting my roots.not every1 does but i have my plant pots in trays and i bottom feed so that would be the way they would drink.(tap roots)

Took the chance and trimmed the roots 2 days ago. There is no reaction from the girls. Like I said, I had lots of roots from the cloner (a small fistful of roots on each one).
I was afraid of rot and pests getting to the exposed roots. So far no one is wilting etc.,.