I can guarantee that updated SC DS Two will run both on 9.4 and 4.2 units (I have 2 "legit" systems and 2 with gateway).
In versions 5.X till 9.2 you will need to re-run the web exploit everytime you reboot your system (entering system configurations and exiting it counts as reboot), if you downgrade your system you can run the web exploit or do the DS Profile Exploit (using your SC DS Two or the blue gateway card).
The DS profile exploit won't require you to reinstall it every reboot, but if you boot any DS retail card or DS flashcard (R4i/blue gateway, SC DS Two) then you will need to reinstall the exploit before using Red Gateway again. It happens because the system will fix the DS Profile every time you enter DS mode.
damos1212 there is a CIA that downgrades the 3DS whitelist, so you can run older DSi compatible cards on it.