I'd say no unless you are a shuffle tracker
I play at some local cardrooms with same rules and pen, but 2 use machines to shuffle the 6 decks, then deal out of a shoe, 2 others hand shuffle the decks, then deal out of a shoe. I've noticed no particular difference in how often I run into favorable counts at the different places.
Don't know if actual studies have been done (I recall a posting a while back that suggested some studies have been done that confirm no real difference), but my experience is as long as they only use the machine to shuffle the decks, but then deal from a shoe (rather than a continuous shuffle machine), it seems to make little difference. Also, remember that the BJ sim programs basically "machine shuffle" the deck when they computer mathematical edges for rules and counting strategies.
But, if you like to shuffle track, obviously you need the hand shuffled games. I suspect a shuffle tracker would look at machine shuffled shoes in the same way a card counter would look at continuous shuffle machines and not want to play them.