Yes, the controller can choose, there is a similar ruling for Cross Counter vs Stone Statue of the Aztecs that will allow the turn player to determine who is actually negating the effect when it comes down to that.
The difference between Horus LV8 and Dark Lucius LV8's summoning though is in the card text. There is nothing in Hours LV8's text that links it's effect to how it was summoned as with the text of Dark Lucius LV8
Dark Lucius LV*
Text:
If this card was Special Summoned by the effect of "Dark Lucius LV6", your opponent's monsters that this card destroys by battle are removed from play, and their effects are negated.
Hours LV8
Text:
This card cannot be Normal Summoned or Set. This card cannot be Special Summoned except by the effect of "Horus the Black Flame Dragon LV6". While this card remains face-up on your side of the field, you can negate the activation and effect of any Spell Cards and destroy them.