Let's see if I can make things a bit more clear than those vague replies earlier...
Darkcorp (1.1 is the latest, AFAIK) is cioscorp, but a newer version. The thing isn't "bad", but it's the way that it does its thing that isn't very ethic. Basically, it is a whole bunch of IOS'es and cIOS'es, hacked and updated to a certain version ("the latest"...at the time of the release date of darkcorp). At that time, it is perfect. However, as newer versions of IOS'es or cIOSes come out, things can get a bit messy. They overwrite the older version, or they do NOT overwrite because those older versions have hacked numbers that make the wii think it IS the latest, and so on. And because those hacked versions aren't built for decent stability with the newest homebrew channel (1.0.8), it can be considered bad.
...unless you're not thinking of updating HBC, and you're perfectly fine on whatever version you have (1.0.5?).
The more important question is: why do you need it? It says in the description pretty clearly that it's purpose is to allow for backup disc loading from the main channel. If you're using an USB device, it helps nothing. And I mean that literally: it helps NOTHING. It doesn't speed up the drive, add compatibility or anything. All that stuff is taken care of by the cIOS'es you're using (latest version of hermes is 20, and Hermes is at 5.1, IIRC).
As for your other questions:
-4.1 fixes one bug in wii sports resort. Hardly worth doing the update from 4.0, as not even everyone has it. But it is still better than updating to 4.2 or 4.3, as those literally have no purpose whatsoever aside making your wii hack-proof. And thus far, no game has a requirement of an update (though I'd say it's best to use priiloader to block games trying to lure you into updating whatever firmware is on the disc).
-if a drive is formatted into wbfs, there is no way to switch to fat32 without reformatting (those similar names are no coincidence).
-afaik, there is no way to load backups straight from the main disc channel (well...maybe sneek is able to do exactly that...I don't have firsthand knowledge about it, though). But with priiloader, you can set it so your wii boots straight into your USB loader. Honestly...I haven't seen my wii menu in months, no matter how often I play on it (well...aside from the couple times I want to change some settings).
-I think you're confusing bootmii with boot2, which is part of the boot sequence of the wii. boot2 obviously can't be removed without bricking, but it can be updated. I don't know how that actually works...I've heard that if you were able to install bootmii as boot2 before, you can reinstall it in case it gets deleted. But don't quote me on that...I don't know for sure.
