Let me get this straight. I'm on 9.0 firmware, and using Ninjhax 1.1 so that I can run CFW. Are you saying that if I simply swap the "boot.3dsx" file for the Ninjhax 2.1 version, I get the added speed benefits of 2.1, with the compatibility of 1.1? Or, are you saying that I can use the Ninjhax 2.1 methods (TubeHax) to run my 1.1 "boot.3dsx", and be able to launch my CFW without needing the Cubic Ninja cart? Either way, that's an awesome improvement, and I'd like to do that. I just need to make sure what I'm doing first.
Yes and no. Here's a step by by step while answering your questions.
1) Make sure you're on 9.2 sysNAND or below. Pretty important, but alot of new guys don't get this.
2) Go to the original Ninjhax (a simple search on Google for "Ninjhax 1" will bring you to the right page - it's the first link) and follow the instructions. Get Ninjhax 1.1 up and running on your 3DS. Install CFWs, CIA installers, the whole nine yards.
3) Follow any one of the numerous guides on GBATemp to creating an emuNAND, linked, unlinked afterwards. Pretty important as well. This step by step assumes you have an emuNAND higher than 9.2 with a sysNAND lower than or equal to 9.2. Otherwise it's pointless.
Alright, so we're done with all that. Next you're going to want to Google "Ninjhax 2" and click the appropriate link.
4) Download the 3dsx file alone. No point in the starter pack. Or maybe you want updated apps. Whatever. You understand.
5) Replace the 3dsx file on your SD card with the the one you just downloaded.
It's as simple as that. As long as you install (follow the steps per usual on Smea's site) Ninjhax 2.1 on your emuNAND, you'll have both on working (Ninjhax 1.1 on sysNAND and 2.1 on emuNAND). This useful tidbit of info is what I gleaned from Zap_Rowsdower. Also from him (and to finally answer your question) no. Ironhax and Tubehax will not work. They don't load the 1.1 payload that you originally installed on your sysNAND (you didn't try installing 2.1 over top of 1.1, right? That'd mess it up. You need the 1.1 CN save payload to make it boot with the new 3dsx file from 2.1). As cool as that'd be, it's no dice for now.
It is nice having Ninjhax working on both systems however.