Yes. But it's the Arm9Loader section of FIRM that handles that. Secret Sector will work just fine if it's encrypted properly first (This is why you need OTP. Though on n3DS, you still need OTP to modify it correctly). It's Arm9Loader that implemented it and bootrom of both n3DS and o3DS are said to be the same. Arm9Loader ends up loading first instead of the normal o3DS FIRM. Arm9Loader is a container of sorts that acts as the gate keeper to the the rest of the FIRM. It's just a different way of loading FIRM and it works just fine on the o3DS provided you install the secret sector before hand. Which is probably why Nintendo hasn't tried to do it via a system update. It would be complicated to try and implement.
First off, it would take two or more system updates to do it safely. First update they have to update NATIVE_FIRM give arm9 new functions for writing to that region of NAND and verifying it. Then actually creating the secret sector. Since Arm9Loader isn't installed yet, having secret sector present at this stage has no impact on the system as it's not used.
Then the second update will update Native_Firm to the new Arm9Loader version of it and the FIRM partitions would be updated accordingly.
If they can't create secret sector in the same go in the first update, then they'd do it in a second update and move off the Arm9Loader install to the third update.
In theory that would work. but Nintendo seems reluctant to do it. Perhaps because it would be pointless because o3DS can be downgraded easily for OTP dump. Of coarse Nintendo didn't know how bad a mistake not locking OTP was when they first made the n3DS because with some tricks, even n3DS can be downgraded to 2.x and lower for OTP dumping. Thus rendering their new Arm9Loader security completely useless.