Without getting too far into my epic spiel about why the STEM push is a silly idea, I think this is off base.
For one, the Academies have traditionally been predominantly engineering schools. Majors, let alone humanities majors, are relatively new to both USNA and USMA.
The STEM push is Navy wide and is popping up in the Army and Air Force commissioning sources as well (Marine Corps...not so much). It's not limited to USNA and NROTC...STEM degrees are being preferred for OCS as well, even in designators where a liberal arts education doesn't matter as much, like intel. Personally, I think this is because:
1: Training for almost all Navy designators out of USNA requires a certain degree of technical or mathematical aptitude: flight school, nuke school, being a SWO, and even EOD and SEALs.
2: Perceived prestige/marketability. For some reason, people think that if you're a liberal arts major you're doomed to live in a subway tunnel. It's a great selling point for the Academy (to potential candidates and their parents) to say that XX% of our students are successful engineering majors. This is especially true when many of my high school friends who attended civilian institutions are unemployed and in danger of living in a subway tunnel, or, worse, their parents. Obviously it doesn't matter when every medically sound USNA grad goes on to be employed for 5+ years and leaves with good employment prospects (which, according to every former officer now employed as a civilian I've talked to, are more because of officer/military experience and less because they took thermo), but I think it comes across as a safety net.
3: This one's kind of in left field, but...cost. Setting up, maintaining, and getting employees for different labs is more expensive than getting a blowhard with a PhD and leather patches on his elbows to talk in a classroom (and, of course, funding his research...which also costs less than the engineering professor's). To be a good engineering school and have mids doing good projects, we need those labs and that gear. But it makes more sense cost-wise to have 20 kids playing with the giant boat-tank than 10.
4: Again, a little out there, but: sustaining the Academy's reputation and "usefulness." We've beaten to death here how much more an Academy ENS/2ndLt costs than an NROTC or OCS ascension. Pumping out a bunch of people with a quality STEM education (see #1) in consistent numbers is a good point for the Academy's continued existence. Known product with a known quality education. I'm not saying that engineers from NROTC schools are "bad," but USNA's engineering dept. is pretty damn good, probably better than many of those other schools.
Edited, again, to add: I'm not trying to downplay engineers and STEM types or say they don't have a place. I personally think there's value to having some enginerds around, and even more value to USNA having a good reputation as a quality school.