Hyphenated names are a single-unit item, and they begin with their first letter.
So your husband is alphabetized until S, for "Smith-Jones."
I don't know about the monograms. You could apply that same argument--he is RLS.
But of course, he's holding onto the Jones for a reason, so my vote would be to never use the monogram style w/ the big center initial, and be "RSJ."
It would look to weird to have 4 letters, though I'm not sure anybody could say he was *wrong*