In the course of randomly wasting time today, I decided to go look at how MPQDraft is doing in terms of popularity, these days. I do that every so often, but it had been a few months since I last looked.
To my surprise, I noted a substantial spike in downloads: 50% more binary downloads and 100% more source downloads, beginning in February. It took me a second to realize the likely cause: SC2 going into beta mid-February. It's not clear to me whether people expect MPQDraft to work with SC2, or whether SC2 has inspired a more general revival in modding.
In any case - MPQDraft does not work with the SC2 beta. There are two reasons for this.
Part of why MPQDraft is so elegant is that it works in a game- and version-independent manner. This is possible because MPQDraft intercepts function calls between the games and the Storm DLL, the latter which contains the functions to access MPQs. This only works if Storm is dynamically linked to the game, in its own DLL. The SC2 beta statically links to Storm; the MPQ functions, as well as others, are incorporated directly into the game executable.
This means the current simple, elegant MPQDraft method will not work, period. The only way to deal with this problem, and to make MPQDraft work when the game statically links to Storm, is to directly locate the function addresses in the game, and include those addresses themselves in the MPQDraft DLL.
The problem with this is that it's game- and version-dependent. Every time a new patch comes out you'll have to wait until I or somebody else updates the function addresses before you can use MPQDraft on the new version. And this obviously requires somebody taking the time to manually locate the functions in every new version, from scratch.
So, that's in the "pain in the ass" class of problems. It also remains to be seen whether Blizzard intends to ship SC2 linked in this way, or if it will dynamically link to Storm in the release version.
The bigger problem is the fact that SC2 is online most of the time, including when you're playing single player (unless you specifically tell it to run in offline mode). Depending on how aggressively Blizzard performs its anti-cheating scans (which they've been doing since SC1), it's plausible that MPQDraft could be detected as a cheat, in which case you'd probably get your account banned.
That's the current state of MPQDraft and SC2.