Great question...
Well where to start to answer this one. Why "deck", why not "deck", why "engine", why not "engine".
First let me say the bottom lines here are going to be:
1) The choice is between two great options because at the end your son will graduate with a degree from USMMA and array of options and opportunities that generally lead to a very bright and successful future.
2) Regardless of which is harder/easier - that is an entirely separate debate and my reaction is pretty much in 90% of the cases if they got into USMMA, they can successfully navigate either curricula and graduate.
3) It really has to be their choice, this is the start of their real journey through adulthood that will continue long after we as parents are gone. Of course we are their parents and I have no doubt in addition to all the unsaid influence we have on them, your child is probably discussing this choice and decision with you, as did mine. You know them well but in the end I found this time in our DS' life - his plebe year - the hardest for me to give him good advice. So often he was really looking for a sounding board rather then a lot of specific advice, he was becoming a man on his own and often I still saw him as a teenager, but truth be told he was much more than that already. You probably saw some of that last weekend, I know we did back three years ago.
Last general disclaimer/point, remember that the current service obligation states:
"Unless a graduate serves as an active duty commissioned officer in the U.S. armed forces or in the NOAA Corps or in a maritime-related position with the Federal government serving the national security interests of the United States, he/she must first seek employment in the maritime industry as a licensed officer aboard vessels operating under the U.S. flag."
So if the economy is such that you can "sail on your license" there's really not any downside more or less to being either a "deck" or "engine" officer. They are pretty similar lives other than your daily tasks aboard the ship and the benefits and drawbacks of a career "at sea" are not too different based on the choice of major. Of course differences do come into play when you look at the shoreside career opportunities.
Now the direct answers to your question the downside of "deck".
Answers will vary but here's my opinion, I was a "Deck" major/graduate almost 30 years ago so that's my perspective.
The first is really the downside of any of the six available majors at Kings Point - they are not - none of them, generic degrees that have a majority of their focus being on teaching the students "how to think" - rather for lots of reasons they are filled with pouring a ton of material into your brain quickly. That's just a function of Kings Point - it's really a six year program crammed into four years: a four year B.S.; one years worth of vocational training on campus; and one year of co-op/internship (sea year). A liberal arts or basic science BA/BS it certainly is not.
The second downside varies by which of the three "deck majors" they choose: Logistics and Intermodal Transportation; Marine Transportation, or Marine Operations and Technology (aka "Shopper"). As your question seems to be rooted in what are the differences in career options for new grads I'll confine my answer here and note that the downside of deck vs. engine is generally more pronounced right now in this economic down-cycle then it is during an up-cycle where just being a USMMA graduate generally left all new grads with multiple good offers in June.
I would first say if they want to go active duty there's not much difference in the midterm and they could get some input and advice from the on campus liaisons as to what impact their choice of major will have on their career as a Junior Officer.
Assuming that's not your focus and it's related to your career choices as a new grad in the maritime industry my "gut" and basic feel is that the biggest drawbacks come with the choice of so called "straight deck" - Marine - as a major, if you aren't thinking about getting either an MBA or JD relatively early in your career (in which case its a GREAT choice.) In the case of a Marine Transportation Major, private industry is apt to look at you for shoreside employment as very similar to a Business Major graduate from any good program with a solid co-op/internship program. Outside of course the "Kings Point Family' which I think we have to leave aside in answering this question. In the case of "Shoppers" - you'll likely be looked at as having a "weird" degree, some especially A&D companies might like that you have some technical courses and practical experience to back it up, other companies will look negatively to the fact that getting those courses in was at the expense of you receiving some introduction to financial analysis, etc. Logistics and Intermodal Transportation grads are likely to looked at and compared to grads from good Supply Chain Management program grads from places like Penn State, Emory-Riddle, etc.
Now compared to Engineering majors this type of downside translates, IMO as follows. Compared to engineering grads, especially those with the ABET accredited degrees: Marine Engineering Systems and/or Marine Engineering and Shipyard Management, new grads in the "Deck Majors" will likely be looking at starting salaries that are 15-20% lower and fewer choices/offers in today's market (which may not persist through 2015 - I know I hope things improve by then). The engineering grads will be compared generally to young grads with B.S.M.E.'s That's not a bad thing and in large part the reason why for last year's Plebe class (2014) almost 75% indicated they wanted to go "engine". However as you noted the engineering curricula at KP is very hands on and practical in it's areas of study and the shipboard jobs are at times hot and dirty. If working literally inside a large slow speed diesel engine puts a smile on your face then KP is one of the few places your time studying engineering is where you'll have a smile on your face. If you'd rather have a career seeing the world looking out the bridge window and trying to see how to make sure you operate the ship most efficiently over it's scheduled route then "deck" is for you. I say that because 5 years into a shoreside career, the salary gap for those who are having successful careers tends to be negligible when comparing "Deck" vs. "Engine".
Its corny but I wouldn't sweat it too much (choice of majors). Truth be told is most of my peers like myself "30 years out" are well into our second or third careers and the biggest things we learned and got out of USMMA are not related to the specifics of our majors or degrees but rather the qualities and things we learned related to leadership, perseverance, self confidence and teamwork.
Hope this helps.