I think the most visible case of this happening is the deck-building game Dominion, where the policy was that it was fine to have free versions so long as they didn't use the artwork and so long as they're taken down when there's an official app. (Which has now happened on some platforms and I think is expected to happen on others soon.)
I also suspect that Vassal is so niche that most designers/publishers don't really see it as taking away very much from paid apps, even if those do exist. The people playing on Vassal are generally the kind of people who buy a lot of board games.
Looks like they discourage the use of artwork and text, but dont actively self police.
"The vassalengine.org web site owners do not verify whether or not uploaded modules contain copyrighted materials. However if the owner of copyrighted material makes a request, we will remove a module from the web site."
But I could potentially see lost sales of tablet implementations of board games; although those almost always codify the specific rules and logic of the game so again quite different to Vassal.
Like for example, Carcassonne: http://www.vassalengine.org/wiki/Module:Carcassonne