Fan made tools have existed for years that would import a folder filled with models inside sub directories and build the import manager settings to match. It is possible in both WEX and JNGP, although JNGP had a drop-down menu option for it. I can honestly say if your project ever gets large enough that you actually want to search through the models inside it with an MPQ browser, putting everything at war3mapImported seems silly.
I guess as long as we live in a world where the fan made tools to strip paths would be considered untrustworthy, and people wouldn't be certain that a "modified" uploaded model wasn't exactly the same, it makes sense that if you trust nothing believing that "change" in an uploaded model is bad makes sense to me in a way. But, from the standpoint of editing models, it doesn't make sense to me. Every time I open and save a model in my software, it reorganizes a few things, but was supposed to suffer no data loss. This was more true of the MDL parser I wrote long ago than the MDX libraries I use which were not written by me.
I try not think of the reorganized file as having been changed. Thinking on that low of a level is like giving up in the idea of software itself to me, at least conceptually. To me, believing that all change is untrustworthy was how I lived and how I made Warcraft III models in fourth grade before I was taught programming. But it is not how I want to live anymore.
If you believe that altering binary bits in an uploaded file is simply wrong and feels bad, I must admit that automatically changing all paths in an MDX when saving to "war3mapImported/" to me feels simply wrong and bad. You're absolutely correct it would improve import time. But to me, if you wanted to improve import time, the correct solution is to change the world editor to import a model and its linked textures from its folder all at the same time, with one click -- and then to import those textures with the correct paths, which it will be able to see at that time.
Cooler idea: new fan made file extension, .tftmdx which includes textures and the model file all in one binary, with correct paths. Then, HiveWE could get it right when importing, better model editors could get it right while editing, and the Hive's online viewer could get it right.
Then there are some people who will run WorldEdit.exe on Windows XP. We don't need to worry about supporting them, because the only users who should choose do so should be people conscious enough that they're supporting themself that they could break a .tftmdx into it's components and import them, and assign correct paths.
@Ralle does the Hive have any policy against nonstandard use of it's servers? For example, suppose that I decide to make etheller.com/hive/upload/model so that even if your users believe strongly in choosing their own MDX paths, I could have my own upload page that cures the model then uploads to the Hive's upload page. Is this a violation of anything, or is it acceptable? ( I would just use an HTTPs library and proxy the user's request to the Hive as though they had uploaded manually when they were finished uploading. Obviously this would require entering user credentials on a foreign non-Hive site so it's possible that I would be the only person using it )