Only thing I know for sure about homebrew apps that use WiFi is that SSID reporting MUST be enabled in your router. That is not the case for normal DS games, or the DS Web-Browser, only homebrew. Don't know why.
I imagine it's the same deal with WEP encryption, it must be disabled for homebrew apps/games. But I never tested that theory. My guess is that homebrew doesn't use the WiFi settings you configured in the DS for your mainstream games/apps, or doesn't access them properly to work on secured networks.
All I know is that in my wireless setup, I have SSID broadcasting turned off and WEP encryption enabled. My games and the Opera browser work that way, but DSOrganize does not.