Based on the source I think you're referring to (mentioned in a sibling comment), it is 40%, not "most". Further, it is clear that height restrictions are a minority of that.
I think it is clear that zoning is a primary cause of NYC's housing problems, but I just don't see any evidence that height restrictions make up much of the problem (remember, the upthread claim I took issue with is "height limits are the only reason there's a shortage of housing").
Anecdotally, a lot of buildings for sale (in Brooklyn, at least) list both the number of apartments and the max it is zoned for. This is relevant because it isn't actually that expensive the reno a 3-apartment into a 4-apartment (no need to tear it down), so zoning ends up being the primary roadblock for people who want to do that.