Being a huge fan of Soma, that's some good inspiration to have :3 The only thing I'd be truly concerned for though, if you chose this route, is how longevity the game will have. Once everything's out there on the net, it kinda feels like it's time has passed. I kinda feel that way about most games that have hidden files; It's a collaberative effort that once solved, has had it's day as far as the general public is concerned. As much as I love Soma (Seriously), that game is no exception to this stigma. Speaking as candidly but sincerely as I can on this, I feel this game deserves a much better fate than that. While I have no illusion about the effort & time it takes, I strongly believe that it would benefit greatly from that little bit of extra TLC, to make it as much of a literal 'Single player' experience as possible in this day & age.
Also, I'm not saying you haven't already put TLC into this... Just making that one very clear.
I'd like to offer a few other examples of in-game rewards, since there's a lot of possibilities with this. Lets pretend for just a second that these ideas wouldn't be a whole other workload that would most likely need to be done as an update/expansion, once the main game is finished;
- Metal Gear Solid: There's always been a bit of interactivity with the unlockables in that, ie; Cutscenes are available in the Movie Theatre, in which you can run around as the main character to choose & play whichever cutscene yourself. They also play around with that in MGS: Special Missions (Photo mode), so there's plenty of room with at least the concept.
- Tomb Raider Anniversary: Find secrets & relics, and finish the levels to unlock character bios, art galleries, commentaries, cutscenes, music & miscellaneous extras like this really cool showcase of all the evironments & their assets (Style Units). Once you've finished the levels, beat them in Time Trial to unlock cheats (Complete an entire chapter, unlock 2 at a time). If anything, stuff like that can be good for hammering in just how much work something of this scale needs.
- Mass Effect 1: After getting achievements for completion as one of the classes you can choose at the start (Soldier, Vanguard, Adept, Sentinel, Engineer, Infiltrator), you can play again as a different class, but with all the skills from the previous class now available (Beat the game as a soldier & choose to be an Infiltrator on the second run, all of Soldier's skills & weapons can be used). I know this isn't an RPG, but the principle of this is interesting to think about, and I've never seen another game do anything like this.
- Metroid Prime: Best not forget these! Stuff like artwork gets unlocked simply by scanning stuff & collecting info (25% complete, 1st gallery open, etc). Simple, but entirely worth remembering in this case.
If I think of any other examples, I'll err... I dunno, there's options available.
This is a lot of info for something that's probably not intended to be thought of as much as I am, and I'm well aware that some would be more tricky than others to think of a suitable use for. The point of this is to give you the info for nothing more than brainstorming. Who knows, you might get an idea or two from one of these & put your own little twist on them. It helps things gain identity & stand out just that little bit more. But at the end of the day, it's all up to you & I'm just someone typing walls of text about this stuff ^^;