Something interesting to report. It appears to be possible to enable slot-1 access from a DSiWare app. I tested this with Sudoku. I did a quick demonstration video here:
Of coarse in this case wooddumper still fails to read the card. This is probably because it's not coded to operate correctly in DSi mode. I only used it to see if there was a change in it's behavior. It looks like I got Slot-1 working because in that test woodumper would show a random card ID value on each read attempt. But if I eject the cartridge (I used a Mario 64 DS game as a test) it would always report this as 0.
I confirmed this new behavior was a result of my modifications by trying it again but with original unmodified Sudoku. Regardless if the cartridge was inserted or not, in vanilla Sudoku environment, wooddumper would always report cardid of 0. So it definitely looks like my changes did something!
I modified Access Control settings at offset 0x1B4 (4 bytes long) to match that of TWLNMenu (the equivalent of DevMenu on the DSi, and yes I already tried to get that to boot on my 3DS. Looks like all dev apps fail to boot on retail consoles. Still haven't figured out why).
If you want to test this your self, these were the bytes I changed it to on Sudoku's access control (offset 0x1B4 in the SRL header): 1B 61 00 00
Also, not sure if this was a factor or not, but I also changed offset 0x0C to be 0B. This setting corresponds to what that's set to in the DSi Launcher SRL. (TWLNMenu also had it set to this).
If you decide to modify that byte, be sure to correct the header CRC.
Slot-1 is active it appears, but whether or not valid data can be retrieved can't be tested yet. There is no (public) DSI mode homebrew that is coded to access slot-1 properly in DSi mode. That and there's a possibility that the sudokohax payload it self might interfere with it. (I heard they had anti-piracy code. DSi NAND keys were destroyed on startup of the Sudokuhax payload. I don't know of any other measures they added. Maybe they actively messed up slot-1 access somehow, But Sudoko doesn't normally have slot-1 access, so I don't see this as likely)
So conclusive tests could not be done.