cIOSes are not what we need to worry about. They can be modified (as long as the author is around, or the source is available) to install to other slots. Then, it would be up to the loaders to add the ability to adjust to use the new slot(s) for use. IE: 224/225
Hermes has always made his source available fortunately...and his cIOS is everything Waninkoko's is and then some.
The real issue is getting a bannerbomb (or Indiana/SSBB exploit) working in v4.2.....and I have already read a confirmation that bannerbomb has been fixed. Next, we have to hope that TT is on this and will fix the boot2 overwrite. That shouldn't be too hard, since the flawed boot1 is the reason we can install it....and since it is a ROM, the flaw will exist in those old boot1 chips forever.
Then, finally, TT would have to install the HBC to a different location.
I don't think we have too much to worry about, except for the fact that all of this will take TIME. So, don't update now unless you would like to be without all of the fun for a few weeks or months