This one I can help with! I did a model of the Hancock some years ago, and in the process did quite a bit of digging in the primary sources.
The best pictorial sources on the Hancock's actual appearance (you probably know this) are (1) the Admiralty draught that was made after her capture by the British, and (2) the series of four oil paintings by Francis Holman, now in the Peabody-Essex Museum of Salem, Massachusetts. Back in the late seventies, right after it acquired the paintings, the museum published a book, Fired By Manley Zeal, by its then maritime curator, Philip Chadwick Foster Smith. (I imagine you have a copy; if you don't, you're in for a treat.) That book contains good reproductions of the paintings and the Admiralty draught. The latter has also been reproduced in the American Neptune, and, come to think of it, in the series of articles I did for the British periodical Model Shipwright, back in 1982-83. (My memory is, as usual, foggy. Didn't we discuss this in the forum a few months back?)
I made the same decision you did, though: I worked from the Chapelle plans, modifying the shape of the bow to match the Admiralty draught. (The latter has a few other tidbits Chapelle didn't reproduce, such as the thickness of the bulwarks. And he added some things, like the gratings on the platforms at the break of the quarterdeck.)
The only info I found about the Hancock's armament was a couple of vague references in the great Naval Documents of the American Revolution series, published by the Navy Department. There's one document (I don't have it in front of me) in which the Continental Congress authorizes the purchase of priming wires and powder charges for the Hancock - some for 6-pounders, some for 9-pounders, and some for 12-pounders. That seems to establish that she carried weapons of those three calibers. On the basis of the proportions of the powder charges in that document, I gave my model twenty-four 12-pounders on the maindeck, six 6-pounders on the quarterdeck, and two 9-pounder bow chasers on the forecastle.
The empty ports in the bow were indeed quite common. They were sometimes referred to as "bridle ports," used for passing a "bridle," a heavy line used to tow the ship or pull her up to an anchor. I have a minor disagreement with Harold Hahn on one small point regarding armament, though. He gave his Hancock two small guns on her quarterdeck, firing through ports in the transom. The plans show openings there all right, but I don't think they're gunports. They're too small, and too high off the deck.
I'm pretty sure she wasn't copper sheathed. At the time of the Revolution the Royal Navy was in the process of adopting copper sheathing; warships got coppered when they came in for refits. I know of no evidence of copper sheathing in the American Continental Navy.
If you're interested, post an e-mail address and I'll be glad to e-mail you some photos of my Hancock. It sounds like you're taking a different approach (mine is solid-hull, rigged with furled sails, on the scale of 3/32"=1'), but it's sometimes useful to see how other folks have dealt with research and modeling problems.
Good luck. She makes a handsome model.