Generally this is fine for apps, just don't use mymenuify mod on vWii (at least not if u have priiloader installed on vWii, or until mymenuify gets updated, use csm installer for themes on vWii instead), and also don't try using region change tools like any region changer or Korean kii
Don't go installing wii ios or system menu wads on vWii though. I think u can still recover using decaffeinater for WiiU but it's a pain you probably want to avoid.
Btw, in case you weren't aware u can just drag and drop your sd card or usb drive letter onto modmii.exe and it will check for updates for any supported apps it's detects. And just wait until my next update, I have a few related surprises up my sleeve you're sure to enjoy. Heck msg me if u want to beta test it just for fun, even though it doesn't really need testing (at least not the surprise I'm referring to)