Wii problems updating
If you manage to get homebrew back, make sure to turn off update checks and disable Wii Connect24 in Wii Settings so this doesn't happen again.
UPDATE 8/3/17 am: As promised, we've spent a couple more days getting to grips with the performance profile of The Legend of Zelda: Breath of the Wild on both Switch and Wii U, and while it's still difficult to justify investing so much money in a new console just for one title, what's clear is that aspects of the game that truly stress the GPU can see significant performance advantages for the Switch title - whether you're docked or using the console as a portable.
You can use my homebrew installation guide to learn how to determine which homebrew package you need and how to install it to your system.
Please note that I have not tried reinstalling homebrew onto a system from which it was deleted, so I can make no guarantees as to the result.
It can also happen if you have Wii Connect24 enabled, as this will automatically install any system updates released by Nintendo.
Updates 4.2 and 4.3 were both specifically designed to kill homebrew.
Wii System Update 4.0Feature additions on your Wii console when it is updated to version 4.0: SD Memory Card Functionality The SD Memory Card functionality of the Wii console has been enhanced to support the following features: Please note that at the time the Wii System Update 4.0 was released, Nintendo made available an updated version of the Wii Speak Channel that supported the SDHC Memory Card format.