That information is all just sitting there on the GC bases. Much of the far ranging smuggling activities, the more ''proactive' outlook is more of a player invention than one founded in the lore of things (Yanagi aside and potential future developments aside. Or so was my understanding while gathering all of the Junker rumors for their part of the wiki).
That being said, yes, the Hogosha would have their merry way with you six ways from sunday, ex military with two bodyguards or no.
Be comparable to a Hogosha being safe as a clam on a Junker base because he's ex KNF with two merc bodyguards.
My route came in to planet honshu from sigma 19 - one trade lane, a quick planet land to swap cargo, and I was out. There are no hogosha patrols around aomori or planet honshu, and considering I didnt go around announcing my presence (and that both sides of the honshu/19 jump gate are GMG controlled - who are enemies with the hogosha) I highly doubt they'd have much forewarning about me being there. Certainly not enough to organize an army to come after my ship.
I know I'm not the only junker who has made RP cardi runs from malta into hokkaido either, it happens all the time.
As far as I'm concerned, as long as it's a quick in-and-out job and there's no hogosha NPC's or players around, there's nothing wrong with a junker popping into kusari for some illicit trade.