Yay. I don’t understand why John dipped in popularity - it was a perennial/timeless classic like William, James and Thomas until a couple of decades ago. These kind of names are great as they have the benefit of making it difficult to judge things like age, social background, even nationality- it’s hard to make any assumptions.
If you aren’t sure then I think it’s fine to just use it as a middle name (to honour your relative ) but personally I love it as a first name - he’ll probably be the only one in his class or possibly even school, yet he’ll have some amazing historical and pop culture namesakes and John has a couple of nice nn’s too (on the off chance he wants one).