Nintendo only says that DSi firmware update v1.4.1U "provides behind-the-scenes improvements to system performance," though Gamasutra notes that many--not all--brands of DSi emulator cards no longer work after the update is applied.
The cards allow users to run unauthorised software, which has legitimate 'homebrew' uses but is demonised for allow pirated games and software to run. Nintendo has succesfully lead pushes to have the cards declared illegal to sell in Japan and the UK.
Nintendo is a little more candid about the Wii firmware update, saying that "Because unauthorized channels or firmware may impair game play or the Wii console, updating to Wii Menu version 4.3 will check for and automatically remove such unauthorized files."
As with the DSi, Wii modding and hacking can allow users to run legitimate homebrew applications but also enables piracy.
As a bonus, it also brings the Wii "some behind the scenes enhancements that do not affect any prominently-used features or menus but will improve system performance."