Neo. The Only. The One.
THE ONE
Yes and No. As far as I can remember, no Targs with black hair sat on the throne as King but, there have been dark haired Targs in the family. So yes, people would snicker but, ultimately, it wouldn't really matter. The only person who would be against it is Aerys and if Rhaegar had won at the Trident, he would have put Aerys in a Medieval insane asylum or had him imprisoned.
Him getting another woman pregnant would have been the bigger deal. Rhaegar would ultimately have to choose who would become king out of Aegon or Aegon (Jon ) and it could have been another DOTD in the making later down the line.
So in the other timeline, you think Jon would have tried to get the throne?
An ambitious Jon Snow in the cut is a scary sight