Dentist told me that my roots are the deepest she has ever seen, is this an issue?
I don't think so. But I would be extra careful about keeping your teeth in good order, as I suspect a root canal might be a bit more difficult on you.
You say this was your first X-ray in years. I hope that doesn't mean it was your first visit to the dentist in years. We all need to get our teeth checked at least once a year so that any necessary work can be done while the problem is still at an early stage.
I think id go to a different dentist with more experience, I wouod not let anyone touch me who noted they never seen it before.