I dont see any discernable difference in the nacelles, they're still toothpicks on a potato. As for the shuttlebay, why then is a quarter of the ships interior given over to shuttles? It's a small ship, not a large carrier or freighter, so why would it waste so much space on shuttles? Much larger ships dont carry that many shuttles because there's little need for them. I bet if you asked the crew if they would prefer more living space or more garage space for shuttles they'll rarely use, they would pick living space.
I am guessing you've done it because shuttles are cool and you can have all sorts of cool stuff in there, not because they're needed. With transporter tech, shuttles are just a backup and were only used in the series when they wanted to get someone out of the way so they could be captured or put in danger. Imagine if a quarter of any of the Enterprise's was nothing but shuttles?