Kurtz said:
Pretty much anything touching the barrel will effect the barrel harmonics in a negative way, even if they're firmly mounted to the barrel (such as the sights, or the handguards). That's why improved stock beddings or even free-floating the entire barrel is common today. This was not unknown at the time either, which is why the swiss used a partially free-floated barrel on their k31 rifles.
The bayonet causing less accuracy idea is only partly related to how the rifles are sighted in at the factory. Even though adding or removing the bayonet will change the point of impact (a grouping will be in a different spot with or without the bayonet), adding a bayonet that contacts the barrel will make each shot less precise (ie more deviation, it'll shoot a larger group), even if the rifle is sighted in with the bayonet. Whether the group will be noticably larger out of a mosin-nagant or k98 is debatable though.
I was going to mention free-floating barrels but you beat me to it. All modern sniper rifles have free-floated barrels.
There are many things that effect where a bullet will land:
1) Ammunition (caliber, grains, powder charge, quality, bullet type, etc.)
2) Wind (especially over greater distances and with lighter bullets)
3) Barrel heat (when barrels get hot, accuracy decreases)
4) Shooter skill (obviously)
5) Sights and optics (because this affects the aim of the gun)
6) Rest (firing from sandbags, from a bipod, prone, off-hand, etc.)
7) Barrel wear and condition (rifling, crown damage, dirty, etc.)
8) Type and make of gun used (obviously)
9) Pressure against barrel (free floating, bayonet, etc.)
10) Muzzle brakes and flash hiders
And much, much more...