As you already experienced, Destiny is a meticulously crafted game despite its shortcoming. Almost all object in Destiny have meanings, including those useless boxes in the Tower.
So, today i was bored and wander around Tower. There i found some stuff, left behind the secret factions
---
[b]**FOTC - Force of The City**[/b]
Turns out, they made the security measures in the Tower and lots of electronics: Anti-air cannon, Security Camera, Jukebox, computer/thing, generator, box.
Now the question is, where are they? Why they made so many important stuff and they just disappear?
The logo looks like speaker holes but in destiny, speaker holes did not looks like that. As you can see in Jukebox where there's the logo and speaker holes in close proximity. That pattern/logo also on boxes that should have no speaker.
---
[b]**7 Seraph / CSFC**[/b]
CSFC acronym did not have "SS - Seven Seraph" but their logo have 7 O (blank circle). Maybe it was "S" on the blank circle?
---
[b]**Tetris**[/b]
They made lots of containers/boxes. Dunno what their faction name is. I have not found any box with the name label :(
---
pardon the editing, im still learning the PS4 video editor.