Going to bump this as I’ve noticed the same behaviour. I’m not sure if this is intended or something that’s been overlooked.
As a fellow moderator, I feel as if votes should still merge into other topics regardless of voter visibility. From my view, votes should still merge regardless of whether “allow users to see who voted” is checked. There are a lot of topics which require merging and some users have already voted on those smaller topics. When merging those to a main topic, it’s a shame to waste those votes and tell them to recast. It may seem logical by not merging votes if set to private, however we’d prefer the privacy on user votes for a number of reasons. It seems slightly odd to me if they only merge when shown to the public when there are private voting settings.
Even an update on this would be appreciated. 
Is this something that could be changed?