I know a couple of people who live in Newport and love living there. But they like it because it is close to their work and to the beach. Newport doesn't have too much of a town center to speak of. If you're looking for a community that is like New Bern but smaller I'd recommend Beaufort. Very quaint, a solid year-round residential community, lots of folks in your age range, close to more normal "city" amenities, and of course fantastic water access. Downside can be cost of housing depending on where you want to live.
Flooding can be an issue anywhere in eastern NC (look at what happened to Havelock last week!), so I really wouldn't let that put you off. You can get data on whether there has been a flood in your potential neighborhood, whether you are in a flood plain, etc.
My perspective is this: if you want to live near the coast, you just accept that there is a potential risk with storm damage (wind and/or flooding). Your homeowner's insurance will make sure you pay for coverage ($$!)!
I would rather choose my community based on those 355 non-risk days, rather than basing where I live on the few days out of the year where something could maybe go wrong.
Hope you find what you're looking for.
