How come a whole bunch of spells, for example rogue’s Pistol Shot and Saber Slash, while obviously producing some sort of visual effect, are nowhere to be found in SpellXSpellVisual.db2? Is there another table responsible for them?

It is likely that a blizzard will use SendPlaySpellVisualKit to send a visual effect. Or SendPlaySpellVisual for missile trajectrory.

And there is another version: Blizzard was fixed using hotfixes base, but was not touched in the client files.