I have to go with Jame.
IMTU, you rarely see the navy with small arms. Sure, there are a few laser rifle in the arms locker, and the occasional officer might have a revolver - perhaps with green bullets.
For Imperial troops, the standard long arms is the Gauss rifle per book 4 mercenary. When the battle dress gets put on, it's the big stuff.
Merchants are shotguns and SMGs. Both are weapons designed to compensate for poor training. SMGs have the advantage of not only being easy to shoot, but being very cheap. For military purposes, the SMG is pretty useless once assault rifles appear (around TL 5-6). Shotguns have sever range limitations.
Pistols are quite handy, concealable and useful if a deal goes bad and you can't carry a heavier weapon.
I don't agree about scouts and the snub pistol. The snub pistol is pretty useless at anything more than the length of a room. It's great for shooting across the parlor of a whorehouse, but anyone spending time on a primitive world, in the great outdoors, is going to find it totally worthless.
Naturally, the independant nature of the Scout service is going to mean scouts are going to carry whatever they feel like, but about the most useful small arms for a scout is probably going to be a medium bore, low tech rifle. Simnple, reliable and capable of dispatching a wide variety of game as well as overly agressive natives.
My vote would be something like a bolt action rifle with a composite stock. Serviceable down to very low TL, nearly indestructable and in a fairly substantial caliber (say 8mm). And something that will not be mistaken for a military weapon at anything over TL4 or so.
A further note about pistols.
I have noted that these are heavily favored in just about any RPG that has them, in preference to superior weapons. I assume this is due to the influenece of popular media where long arms are pretty rare. In my 20+ years of GMing, I have noticed that the players that pick long guns are their primiay weapon are usually either shooters or prior service.
Within the military services, handguns have a minimal role to play. Except in very specific situations, they are mostly just badges of rank, like swords or a swagger stick - and about as useful.
In the Army or Marine, the people who are going to have (official) side arms are going to be officers (sometimes) and MPs, or those strange SpecOps types that really don't count.