They're not particularly happy about homebrewn anything, nor have they ever been. If you want confirmation of this, dig around online for details about the Wii and homebrewn games/demos -- continual firmware updates for the Wii intentionally block homebrew stuff.
EDIT: If you're specifically referring to NES homebrew, my guess is that they're not too concerned with it, as long as it doesn't involve direct copyright violation (copying of sprites/graphics from commercial games), or somehow imposes on the Wii's VirtualWare stuff (which uses an actual NES/FC emulator), especially since that's a form of financial income for them.
Nintendo Co. (Japan) didn't appear to have any problem with MONDO21's documentary called "TV-GAME GENERATION - SPIRIT OF 8bit"...
Part 1/3:
http://www.youtube.com/watch?v=vzXbDcTqZ3M
Part 2/3:
http://www.youtube.com/watch?v=x9FJK8F6a-w
Part 3/3:
http://www.youtube.com/watch?v=QkxFvf1Tx9A
...where a series of dudes got together and made a present-day Famicom game called Mr. Splash. They had to find all the necessary folks (6502 programmer, two pixel artists, and a sound programmer) too, plus had a producer and director. They used publicly-available tools (YYChar, NESASM, etc.) to make the game. Box art, a full game manual, PCB, mask ROMs, and a casing were all made too:
http://www.youtube.com/watch?v=Jm3DSMULStI
http://www.youtube.com/watch?v=k50-R6kESGM
In the case you bought it, you actually got a CD as well, which contained the source code, and a custom-made version of VirtuaNES which only runs Mr. Splash (and the ROM image is embedded in the Windows EXE).
The source was intentionally obfuscated in a couple ways:
1) Filenames/directory structure was intentionally lost (so you have tons of files to edit to fix INCLUDE directives)
2) Palette + CHR data files are actually ASCII dumps of the hexadecimal values, which requires you to copy/paste the contents into a hex editor and save them as an actual binary for INCBIN inclusion.
3) Code does not assemble due to NESASM bugs -- variable names are too long, causing it to segfault (yes really!). Rename the variables to something shorter to work around this. I have no idea how the authors dealt with this in the first place...
I've fixed up all of the source myself, and have been able to assemble/link an actual working ROM image of Mr. Splash:
Code:
12/21/2008 14:15 40,976 001_ProjectF.nes
MD5:
81CD1CC07B694CFB61B77A098D5A6B9C 001_ProjectF.nes
I'd rather not give it out based on the fact that I don't know what the copyright is. My guess is, based on all of the above, they'd rather people not run around distributing the ROM, but actually take the time to go through the pains I did to fix up the source and make their own copy.
Maybe the latter portion of my post should be put into the FCdev forum... heh. :-)