I actually really like the way Henry Kenyon sounds. The repeated "en" sound is like a subtle echo that ties the first and last name together. It's not obnoxiously rhymey the way Henry Denney or Henry Cory might be.
Samuel and Henry are perfect for brothers. They both have sort of an early American feel. They're familiar without being WAY too common.
Henry Alexander Kenyon sounds great. H.A.K. is fine for initials, I think. Most people (if they notice it at all) will think of hacking a computer -- which takes talent and isn't the most negative association. If you do want to avoid H.A.K. for initials, what other middle names are you considering? Here are a few that I like. I like something that is three or four syllables and does not end in "y" or "n."
- Henry Nathaniel Kenyon
- Henry Julius Kenyon
- Henry Christopher Kenyon
- Henry Nicholas Kenyon
- Henry Dominic Kenyon
- Henry Jeremiah Kenyon
- Henry Oliver Kenyon (H.O.K.?)
- Henry Malachi Kenyon
- Henry Theodore Kenyon
One syllable can also sound nice:
- Henry Blake Kenyon
- Henry Jude Kenyon
- Henry Joel Kenyon
- Henry Grant Kenyon
- Henry Graham Kenyon
Good luck!