Yeah, in the case of that full brick, you will lose your saves, and your mod chip, if you don't remove the modchip before hand.
The main benefit of having nintendo handle your system though, is if you bought any VC/WiiWare/DLC They will transfer it to the refurb system. (You will have to redownload it, but it will be for free.). In other words, repair with nintendo, and it costs you, you would only be out $85 or whatever they charge.
Buy a new system, and you would be out quite a bit more than that, if you bought lots of VC/WiiWare/DLC.
The main benefit of having nintendo handle your system though, is if you bought any VC/WiiWare/DLC They will transfer it to the refurb system. (You will have to redownload it, but it will be for free.). In other words, repair with nintendo, and it costs you, you would only be out $85 or whatever they charge.
Buy a new system, and you would be out quite a bit more than that, if you bought lots of VC/WiiWare/DLC.