If Universal wanted to build a dark ride there, or anything else, they would have told the HHN team to scram and find another place.
Villain-Con has just the right amount of space, it's definitely not claustrophobic at all. The only issue is that they placed the dots where you stand on way too close to each other, but it has nothing to do with the space the attraction occupies. That's more of a capacity thing.
While HHN is a popular event, Universal will certainly not let it impact theme park expansions whatsoever. They were very close to removing the FFL theater a few years back for more Potter stuff, HHN team would have had to scramble to find another location for a show.