Too bad I've already downloaded ExciteBike 3D and Pokédex 3D before I linked my account.
Figured I'd offer a little status update on this. About a week after this, I emailed Nintendo explaining my issues linking my Club Nintendo account to the Wii and 3DS shops. It took about another week for a response, but fortunately it was about what I was expecting. The person said that he registered my two 3DS downloads for me, and that they should show up on my account within seven days. It has also been too much time to do the same for my Wii downloads; I've no idea what the cutoff would be, but it's been longer than 90 days on all of them, which is usually the maximum amount of time for something like this.
About nine days after getting that email, which was a couple days ago from the current date, those two 3DS registration surveys appeared in my account. I guess business days weren't counted, but oh well, at least I got them. However, interestingly, all of my Wii downloads appeared in my account as well, with the exception of the WiiWare demos. I also received the survey for the Wii Netflix download, so I got a little more than I expected to get.
It's nice I won't miss out on the coins for the 3DS games, but I probably could have gotten around 150 for my Wii downloads. Oh well, I have no real proof that I had a linking issue, so I'm just glad I got anything at all. Plus, if I really cared about those coins, I would have tried to solve this issue much sooner than I did.