Some skills like linker’s electric shock can be used with both dagger and pistol while some are locked to either dagger or pistol. If you’re going to choose bullet marker and then assassin, you’d have to invest in both dagger and pistol since assassin skills need a dagger to be used and bullet marker skills need a pistol to be used. If it’s for something like a linker-enchanter-bullet marker, then only investing on a pistol is fine.
As for swords, it’s the same reason you invest on dagger/shield for other classes. People still use good swords because of the stats you get from them. And enchanters, in particular, still use wastrel sword because of its special effect that works with lightning hands.
Anyway, for scout, just consider that all of their skills are based on subweapon (with a few skill exceptions in corsair and squire).