From personal experience, injecting heaps of custom VC's, Project M being one of them, installing games to system NAND will be fine and wont cause any issues.
For those that say, don't install games to NAND or any online tutorials that advise you not to. Don't listen to them, it's perfectly fine, I have games installed on my system NAND since day one when WUP/USB installs was figured out and not have any issues.
Please be aware that when injecting Wii games, it's always best practice to try and make sure the Wii game is the same region has your WiiU console. In some cases, if you inject an out of region Wii game, it may boot to black screen. This is due to the Video Modes that's included in the game, some game devs have encoded both NTSC and PAL video modes for their games and this will work on both regions. There are some devs that just encode whatever Video Mode the region of the game is released in causing the game to boot to black screen if it can't find a suitable video mode.
If this is the case, if your using TeconMoon's WiiVC Injector script to inject your Wii games, under the ADVANCED options menu, right down the button there is a "Patch video mode with Wii-VMC....." option that you can use to try and force the correct video mode for your inject.