Becaus the Maquis ID can treat any lawful trader as a combat target, not just a cargo-piracy target (IE. to prevent Gunboats from insta-killing transports). However, this change was implemented before SNACs got nerfed and GBs got buffed, leaving the Maquis horribly under-equipped to deal with GB-dense enemies.
There is no supporting lore-related reason. They may be terrorists, but they're supported by the Council, which is not short on ships at this point in time.
