Hm I was unaware of those crates in in the Nod's TD campaign, I really need to play that game badly. But I approve collectibles like this, having extra weapons in the next or very last mission. But I'd also like to unlock some cool stuff like the ones I said in my first post. And yeah the Intelligence Database could be updated with the collectibles, so my idea can easily combine with the unit customization and Intelligence Database.
If a collectible is hidden TOO well, the player can always use Youtube for clips to see where to find it, like I mostly do. Or they can simply ask someone in the online channels for information where that collectible is.