Let me be a *CENSORED* a little.

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B) This is a more complicated situation. The two "Mystic Tomato" will activate in the same time therefore the will form a SEGOC (Simaltaneous Effects Go On Chain . In a SEGOC the turn's player's effects are being placed first in the Chain so it will be like this.

Chain Link 1 : Player A's "Mystic Tomato"
Chain Link 2 : Player A's "Light and Darkness Dragon"
Chain Link 3 : Player B's "Mystic Tomato"
---Chain Resolves Backwards---
Chain Link 3 : Player B's "Mystic Tomato" resolves succesfully
Chain Link 2 : Player A's "Light and Darkness Dragon" negates Player A's "Mystic Tomato"
Chain Link 1 : Player A's "Mystic Tomato" tries to resolve but is negated.

uhum, does the spell speed issue already considered in this scenario?

LaDD effect is quick effect (spell speed 2)
Mystic Tomato is trigger-effect (spell speed 1)

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Also for the question A.
A) "Light and Darkness Dragon" is a quick effect monster so his effect can only activate ONCE per chain . Since his effect is mandatory it will activate and negate the first card that was activated immediately so the chain will be like

Whaat the FUACK.

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The ability of "Horus the Black Flame Dragon LV8" to negate Spell Cards is a Quick effect that must be chained to the activation of the Spell Card. You can activate this effect multiple times in the same chain to negate the activation and effect of several Spell Cards that are activated in the same chain.[1]

The only reason why LaDD only negate once-per-chain is Because Konami Says So.(well to prevent an infinite loop as well though probably)

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Chain Link 1 : "Compulsory Evacuation Device"
Chain Link 2 : "Light and Darkness Dragon"
Chain Link 3 : "Bottomless Trap Hole"
---Chain Resolves Backwards---
Chain Link 3 : "Bottomless Trap Hole" destroys and then removes "Light and Darkness Dragon" from the game
Chain Link 2 : "Light and Darkness Dragon" negates "Compulsory Evacuation Device"
Chain Link 1 : "Compulsory Evacuation Device" tries to activate but its negated

not a big deal, but compare out this ruling:

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If "Magic Jammer" is chained to "Geartown", "Magic Jammer" resolves first and negates and destroys "Geartown" as Chain Link 2. Chain Link 1 does not resolve since "Geartown"'s activation was negated. The last thing to resolve is "Magic Jammer", so you can activate the effect of "Geartown" and Special Summon an "Ancient Gear" monster.[2]

my point is, if an activation is negated, the negated chainlink completely disapear for timing issue.A different situation if only the effect is negated.

also, there's this ruling:

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“Light and Darkness Dragon's” second effect that negates the activation of Spell, Trap, and the effects of Effect Monsters is a Quick Effect. “Light and Darkness Dragon” loses 500 ATK and DEF when its effect is resolved, after negating the activation of the Spell, Trap, or effect of the Effect Monster. This effect can be activated during the Damage Step.[1]

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If the ATK and DEF of “Light and Darkness Dragon” are less than 500 when a Spell, Trap, or effect of an Effect Monster is activated, the second effect of “Light and Darkness Dragon” will still activate but when it resolves it will not negate the activation of the Spell, Trap, or effect of the Effect Monster because its ATK and DEF cannot be reduced by 500.[1]

-> LaDD does not able to negate anything because his atk/def can't be reduced by 500 (it's removed).

Give me Warning
it's expensive for me to buy...>_>