Good play through! I've never encountered the secret underwater terminal, that I recall. I had to chuckle when BS had you read the terminal. ;)
If you look at the starting terminal, you will see a V shaped notch in the top of the map. There are two hidden doors, one on each side of the V shape (in map view, the top/ inner portion of the V looks like negative space).
Tab along the wall there until you find one of the doors. Inside are a few rooms; one containing a save terminal. The main room contains a low enclosure in which a 2X pick up sits. Look around. Notice the corner pillar which is similarly sized and shaped as the low enclosure? How interesting. Tab it to activate it. First it looks like a solid platform, but it turns out to be an enclosure which lowers down. Inside it is an SMG and lots of ammo for it.
Of course, such a nice find requires a guard. :-)