Hmm...Well before the end of last month I sent my Wii in cause of GPU artifacting. I deleted all visible signs of Homebrewing. It was under a new warranty from where I had sent it in back in March for a Disc drive repair. When I sent it in recently I sent in with Bootmii/boot2 on it minus the SD card of course and all internal signs purposely to ease my own curiosity. Several days later I got a call that my system was unrepairable, the representative mentioned that it also failed a test check that 2 illegal channels were found and they wanted to know if I wanted my original system back or a replacement I chose the replacement and received a whole new warranty for my replacement. I kinda played dumb but didn't press the issue of what channels were found or why my original system couldn't be fixed. Why ruin a good thing and they were being nice about it all.
As far as your scenario the warranty has expired anyway and you're paying for the repairs. If anything were to be mentioned just tell them the warranty had already expired so you felt it couldn't really get more voided or expired than it was already so you wanted to experiment a little.