Diseases, particularly viral diseases, are a major problem in vegetatively propagated crops and those are almost all that we grow. I do the best management that I can to detect and eliminate disease, but it is not nearly enough. Every year I learn a little more and get a little better, but eradicating disease from the crops that we sell is a long term process. Most of them have probably been carrying viruses for decades.
When I know that a variety is infected with a particular virus, I note it in the catalog (assuming that it is one of the very common and endemic viruses that we just choose to live with, like Dahlia Mosaic Virus or Potato Viruses X/Y and not some rarity that needs to be eradicated). I do my best to eliminate any varieties that are obviously and seriously sick and that have depressed yield or other symptoms that make them undesirable. The lack of any mention about disease is not an indication that the variety isn’t carrying one; it just means that I don’t know.
I would eventually like to get to the point where I can periodically test everything on a regular schedule, but the cost runs into the tens of thousands of dollars and exceeds what we make in a year, so, for now, I make incremental improvements as I can. I don’t think that we are particularly unusual in this regard. One of the benefits of testing has been that I can see that much of the stock that we have purchased from other nurseries is also infected with viruses. Virtually every dahlia and non-certified potato that I have ever received has been infected with something, to the extent where I just no longer even bother to acquire either one anymore.
If you are concerned about viruses, the best practice would be to grow from true seeds instead of roots/tubers. I can’t even guarantee you that true seeds carry no viruses, but the likelihood is much lower and we take precautionary steps with our true seeds like heat treatment and surface sterilization to reduce the risk.