So Custom Weapon Bonuses automatically apply to currently made weapons?

Does my currently built Shishkebab automatically have the bonus from my Shishkebab v2 schematics?

No, it doesn't, but there are no weapon attack/damage bonuses gained from getting multiple copies of the schematics. The 'effectiveness' in this case is actually regarding the 'Condition' (or 'Repair') that the weapon starts in when initially crafted.

This isn't necessarily a miscommunication, as a higher state of Repair/Condition does mean a higher damage output, and therefore a 'v2' or 'v3' schematic does increase the 'starting effectiveness' over a 'v1' weapon. But given that you can bring up your v1 weapon to a higher state of repair by combining weapons or visiting NPCs, your v1 weapon can be just as 'effective' as one built with a v2 or v3 schematic.

This is confirmed on the Wiki:

Additional schematics do not increase the base damage of a weapon. As the base item is the same, the base statistics are as well. The change is in its starting condition (or number, for the bottlecap mine and Nuka-grenade), which does increase the effective damage of the weapon.
_{Fallout 3 Crafting - Wikia}

For non-explosives, crafting a weapon will result in the following starting Condition/Repair:

• 1 schematic - 75% of your repair skill
• 2 schematics - 100% of your repair skill
• 3 schematics - 125% of your repair skill (to a maximum of 100% condition)

For explosives (eg Bottlecap Mine), obtaining additional schematics will give you another item from crafting a single set of components. For example, with v2 Bottlecap Mine schematics, each craft will give you two Mines.