Both. It is a matter of what you are and where you are. IRL we have 90000BRT "big juicy targets" (aks Aircraft carrier) and 1900BRT "mean little killers" (K130 Corvettes) both existing in first world navies.
Same when it comes to cargo craft, there are the extremly huge oil tankers and container ships and on the other end you have the 1350BRT "Europakahn" that is the final waterborn element of the distribution networks
So there is a big navy and huge cargo ships. But those frequent the big ports and high-tech/high pop systems that produce enough cargo and taxes. They can only operate on the high-volume trade routes, they can only operate where the supply infrastructure allows it (You won't see LASH - Lighter on Ship - crafts wilderness refuel, nor will a BatRon do that)
Characters on the other pseudopod are the equivalent to channel ships and a brownwater/littoral navy. They spread out from the large trading hubs, distributing parts of the cargo. Maybe to a secondary hub, where it is again split up, maybe the final steps. When the crew a warship it is part of a subsector (colonial) fleet or an anti-piracy unit.
Think "Master and Commander" or the early "Hornblowers" (and remember, those US Raider Frigates are tough!) or the early Honor Harrington (Basilisk Station, Honor of the Queen). Not Lord Nelson or Honor in "At all Costs"
Scouts are the most problematic. The 100dt scout is not really useful for long range exploration. The Scoutship from the QLI adventure, the Donosev(sp?) or the 3000dt Scout Cruiser from G:T First In are better choices there. So if "to boldly go where no one has gone before" (White paint and Counselors optional) is your idea, you'll have to fill the ship with NPC. The benefit is that you can either use Redshirts or kill off a character and still keep the player in.
Officer: So Mrs. Dax, you are responsible for the mental health of the DS-9 crew
Ezri: Question or accusition Sir?