Here is a link to an interesting book, chapters 5 and 8 are of particular interest for this discussion. 5 is co-authored by Sister Noella Marcellino who is also known as the "cheese nun". A trained microbiologist, her research has shown that the wooden vat is actually safer than stainless steel in regards to pathogens, including Listeria.
Cheese and Microbes
Here are some quotations from chapter 8 of the above referenced book:
"Very few data exist regarding the inoculation of wood by microorganisms."
"Microbial adhesion was dependent on the wood species and microorganisms tested."
"It is clearly stated that surfaces in contact with milk should be easy to clean and well maintained. This requires smooth, washable and nontoxic surfaces. After use these surfaces should be cleaned and, if necessary, disinfected.... Wood porosity clearly does not fit the requirement for a smooth surface and plastic and stainless steel utensils are preferred."
"Currently no legislation or guidelines exist in Europe regarding the cleaning of wooden tools. The only mandatory aspect is to guarantee the efficiency of the cleaning regarding potential contamination by pathogen species."
"In the scientific literature only two [types] of wood vats have been explored."
"All [regulations] support the use of wood without restriction, provided that the appropriate cleaning and drying procedures are utilized. General guidelines for wood management in the dairy sector are missing and would be of great value to the future of artisan cheese production. Many scientific questions remain..."
It seems that my arguments stand as the author's statements support them: No protocol has been developed to maintain and clean wood so as to guarantee that it is pathogen free. Such a protocol would have to kill pathogens without harming beneficial bacteria. Otherwise there is no advantage to using a wood vat beyond the aesthetics of "doing it the old way".
That some Italian cheese making operations are said to have been safely making Listeria free cheese in wooden vats for many, many years is proof of nothing. I quote from the following.L. monocytogenes was not identified as a cause of foodborne illness until 1981, however. An outbreak of listeriosis in Halifax, Nova Scotia, involving 41 cases and 18 deaths, mostly in pregnant women and neonates, was epidemiologically linked to the consumption of coleslaw containing cabbage that had been contaminated with L. monocytogenes-contaminated sheep manure. Since then, a number of cases of foodborne listeriosis have been reported, and L. monocytogenes is now widely recognized as an important hazard in the food industry.