Totally aggreed! Particularly with herpesvirus, as they are masters at remaining hidden (latent) usually in the nervous system where they are unreachable by antibiotics and most antivirals until immunodepression by some other cause allows them to break out (think shingles). So isolating some herpesvirus particles in the faeces might mean that they are at least in part responsible for the disease but on the other hand it may be the other way round, the disease has weakened the immune defences of the fish allowing the latent herpes to proliferate outside their hiding place.
This topic has made me wanting to find more about the so called Angelfish AIDS of the 80's and 90's where in only less than 10% of fish submitted to labs a significant number of viral particles were found, some were herpes but only very few were paramyxovirus that showed some capacity to produce the disease in experimental models. In over 90% of cases the cause was identified as the usual range of nasty bacteria and/or parasites.
Interestingly there was a similar argument on Discus Plague reported a few months ago on Poppa Rhino's website, someone was refering the conclusions of some german researchers that the disease was of bacterial nature and some success had been obtained by antibiotic baths (kanamycin?) while others cited dr Waltzek and the herpesvirus. In neither case though there seemed to be any links to actual published studies. Browsing the few studies about infectious diseases and epidemiology in ornamental fish though it appears that many fish of different species can carry pretty nasty bugs such as Aeromonas, Yersinia (yes the genus of bacteria amongst which is the cause of the original bona-fide Plague), Vibrio and others. Most of them are resistent to sulphonamides and some antibiotics such as Oxytetracycline. It would be nice to be able to tell the exact cause of every disease but as we seem to be in the speculating game my opinion, for what it's worth, is that a discus made very poorly by one of these nasty viruses or bacteria or parasites will look very similar to one clobbered by one of the others: dark, clamped finns, off food, breathing fast, possibly shedding mucus etc. Once one fish gets sick and starts releasing a great number of bugs in the tank these can overwhelm even the other fish that were ok until then. Just my 2C