There no pillaging trade routes in GalCiv 3. There are other differences.

Trade routes have a bigger effect on relations with other civs. Civs can get offended if you're trading with an enemy or a civ with the *wrong* ideology.

You also can't setup a second trade route between 2 planets. You need to setup trade routes between different combinations of planets. This includes routes established by other civs. If another civ has established a trade route between Earth and Drengi, you can't establish your own trade route between Earth and Drengi.

Simple. Conquer either of the connected planets.

Destroy the planet if you'd like to ensure it never trades again.

There is code for raiding, just no UI element to support it. (Its in GlobalDefs)

    <TradeRouteRaidMods>
      <EffectType>TradeRouteValue</EffectType>
      <Target>
        <TargetType>TradeRoute</TargetType>
      </Target>
      <BonusType>Multiplier</BonusType>
      <ValueType>Special</ValueType>
      <SpecialValue>
        <Special>TradeRouteRaidBonus</Special>
        <ValueParam>-0.10</ValueParam>
      </SpecialValue>
    </TradeRouteRaidMods>

    <TradeRouteRaidPathMods>
      <EffectType>RaidBonus</EffectType>
      <Target>
        <TargetType>TradeRoutePath</TargetType>
      </Target>
      <BonusType>Flat</BonusType>
      <ValueType>Special</ValueType>
      <SpecialValue>
        <Special>TradeRouteRaidBonus</Special>
        <ValueParam>0.10</ValueParam>
      </SpecialValue>
    </TradeRouteRaidPathMods>

    <NumTurnsToMaxRaid>10</NumTurnsToMaxRaid>
    <NumTurnsToKillTradeRouteConsecutiveRaid>5</NumTurnsToKillTradeRouteConsecutiveRaid>
    <NumTurnsToKillTradeRouteNonConsecutiveRaid>10</NumTurnsToKillTradeRouteNonConsecutiveRaid>
    <NumTurnsToTradeRouteRecoveryStart>10</NumTurnsToTradeRouteRecoveryStart>