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Maintaining, gaining or regaining reputation with Uguras Armaments and/or the Cartel is possible but it's tricky and isn't really compatible with treating Fields Of Opportunity like other systems. Without wanting to provide too many spoilers, it is worth noting that the TTO-specific mission, 'The Rising Tide' is Uguras Armament-related so it might be worth holding off from war with UA, at least initially.
The pirates will attack any trade ship they find independent of it making sense to do so. Even if you possess 30 reputation from helping them a lot they will not hesitate to take shots at one of your trade ships. Additionally they will see no trouble trying to loot a Lyramekron despite it being considerably tougher than they are. This lack of intelligence is unfortunate and more often than not will lead the player towards war.
Snafu adds:
In v4 pirates now /act/ like pirates: they go for the loot! In the TTO sectors this is particularly significant, as once a Phoenix (taking the time until it has all its drones back) has filled its cargo bays it will fly off to trade its loot (usually) elsewhere; either way, while it does this it won't be attacking <player> or any other ships! This makes TTO sectors less of a potential wipeout loss & more of a (admittedly dangerous) place to set up trade.
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