Well, this may be way too late for you, but I thought I would throw it up here anyway since I haven't seen or heard anything regarding Descendant in a while. For what it's worth...
I served on board the USS Theodore Roosevelt CVN-71 right after it was commissioned. The ship had just undergone Sea Trials and I was onboard during Shock Trials. Sea Trials would have the ship's full contingent of men on board along with civilian engineers as did Shock Trials. The crew itself would consist of seasoned vets along with any new crew assigned to the ship, but no cadets of any kind. At least from my experience. Cadets only came on board during the summer as a type of internship.
Shock Trials for my ship were conducted in the Atlantic off the coast of Cuba somewhere. Shock Trials consist of three "shots" or explosive charges set off in the water. Each being closer to the ship with the third being the closest. Civilian engineers have equipment everywhere monitoring the impact to the ship with each shot. It's purpose is to see what damage is sustained in a "near miss" scenario. We had a raffle for the last shot and the winner got to actually detonate the explosives. Picture of the third shot is here: http://www.zazzle.com/uss_theodore_roosevelt_cvn_71_poster-228839774610080892
As you can see in the picture, no aircraft were on board at the time. We were in full battle stations during each shot. This means we were in condition Zebra. Condition Zebra means every door, or "hatch" if you will, is to be shut and locked down. The idea being if the hull is breached for any reason the water would only be able to fill up the compartments immediately exposed to the breach as all X-Ray, Yoke, and Zebra doors are water tight when closed.
If I remember correctly, the shots were done over about a 6 week period with about 2 weeks in between each shot for the engineers to study the data they gathered. I also remember Jean Dixon predicting the TR would break apart on the third shot and sink.
To answer your other questions: No arms would have been on board at the time. Should something go wrong during either trial, you certainly don't want armament getting mixed into the fray. Plus, you wouldn't want to lose any of your bombs and missiles should something really go wrong. That could easily be millions of dollars lost, then think about the cost of trying to recover all of that from the bottom of the sea or in your case a lake. To see how armament can complicate matters, just Google the fire on the USS Forrestall when a missile somehow fired while planes were parked on the flight deck. A chain reaction took place as plane after plane blew up along with any armament on them, a lot of people died that day. Video here: http://www.youtube.com/watch?v=chuiyXQKw3I
You know what might be cool for your book though would be to arm the USS Freedom with what the US Navy is really wanting to put on their ships - Rail Guns. See the article here: http://www.foxnews.com/scitech/2010/12/10/navy-railgun-shoots-bullets-electromagnet/ Heck, if you're going to take down some unknown biological freak of nature, you might as well blow it up real good!!