Start off with a merchant hull, my suggestion is the Free Trader, the Far Trader, and the Fat Trader. Make the turrets popups, light on the ammo usage, heavy on the damage. Throw out the deckplans except for the basic deck shape. Carve out some cargo space to keep ammo, brigs, and to provide some tonnage to add more armor. Redundancy is a good keyword.
Remember, this isn't going to be a merchant, it's an anti-pirate ship meant to be hired out as protection for convoys.
That's for anti-pirate q-ships. For covert/insertion ops, don't hide the weapons, but list one or more as down for repairs on the ship's papers, with "parts" being creatively broken. For that, you want that somewhat down-at-the-heels look, which is more cosmetic than anything.
Or, just have the "passengers" have good, but forged papers and just be an honest looking merchant.