Interesting question! It seems that a good way to answer it would be to perform a cross-checking of the "List of encyclopedias by language"  with "List of Wikipedias" , . The format of those lists is not easily parsable/comparable, though, so I'll leave these links as pointers for someone wiling to do the analysis.
EDIT: Couldn't resist it. I performed a rudimentary parsing in  and  and used AWB's excellent list comparer tool to match the two sets of languages. It turns out that out of the 260 wikipedia editions, 220 don't seem to have physical counterparts (at least they're not listed in ). I'll put the list in , for convenience.
An interesting detail: there's one <s>physical</s> encyclopedia that doesn't have a Wikipedia counterpart: Leonese , which shares the language code as Asturianu (ast) -- for which there is indeed a Wikipedia, btw.
EDIT 2: My bad: the Leonese encyclopedia is afterall not a traditional one, but a wiki instead. Fixed above.