So I'm playing a Rogue Trader game as an Ork Weirdboy and I have a Minder. I saw that it had the Clan trait but I don't know whether or not it gets the clan bonuses like I do. Does it specify this anywhere or does the GM decide?

No. NPCs don't generally get bonuses that aren't specifically called out; it's there because most orks have Peer (Own Klan) or access to it - hopefully the Minderz are the same Klan as you (which might be useful when trying to convince them to stop rugby-tackling you whenever you want to do something.....)