Moral of the story: DON'T collect dust.
Or collect dust into an old-fashioned single-address wallet or perhaps into a paper wallet. Would that work better? If so, then the moral could be amended to, "Don't collect dust into a HD wallet."
No.
50 inputs is still 50 inputs. It doesn't matter if it's a single bitcoin address or 50 different addresses.
Example.... a 50cent coin (1 input) takes a lot less space, easier to count, move and spend than 50 pennies (50 inputs).