Important Security Note : If you add X Homebrew Game, and link to X Homebrew Game's Server download, then the developer switches out X Homebrew Game for X Pirated Rom, you're still going to be linking to it from your database.
Unless you have complete control, you do not have complete control.
If you're going to do this at all, one important piece of the puzzle is to contact FBI and all similar apps, to ask if they'd redirect their internal database handling to make use of your new database. Also, you're going to need a REALLY good server to keep this all up and running, and that will more than likely prove costly, especially if 1,000 homebrew apps and all of their thousands of users, suddenly switch to using your server's database.
Be very very careful, because that initial spike could seriously cost you quite a fair amount, if your server isn't on a bandwidth cap. (and will vice-versa lead to complaints if the site fails due to said bandwidth cap)
Also, Nintendo will probably come a-knockin', so always be wary of that.
But otherwise, best of luck to you. Just be really careful, and absolutely sure that you're wanting to do this.
All my games can be
found here, with the 3DS icons obviously leading to the zips.