Well i mean you could turn those settings off right? I usually just go to friend list and set activity to private, so that way, no one knows what i am playing. Besides i dunno many people actually concerned with mii plaza or street pass, it seem like two very unused features of 3DS, only few games use street pass, and mii plaza isn't that fun, is more of a thing for people who bought the system without a game at the time. Other than that, street pass perhaps just a way for people to spy on you, but i mean they can't do anything about it.
"Hello, nintendo? Yes, i saw that someone has a game called Rockman 4 Minus Infinity on my street pass, but i can't find it in the eshop.... Yes is right here, it says that on my mii plaza, favorite game, rockman 4 minus infinity.... Well i want that game too. How he get it.... That isn't a game you are aware of? But is on nes, it must be a virtual console title.... I dunno who it was, just the name of the mii says paul1773.... Hello?"
To be honest, i don't think any of that stuff is actually shared online or on any server, is just reading from your activity log, if you constantly delete your activity log it probably will help. Most of that stuff is just broadcasting data from the system, is probably similar to how playstation show what game you playing when on psn and you look at your friend list. It doesn't work for games that are backwards compatible (PS2/PS1 games on PS3, PSP/PS1 games on PSVITA) But stuff like RETROARCH or GENESISPLUS and other homebrew will show up if you check friend list. Just remember to turn off internet access or disconnect from the Nintendo network or PSN when playing that stuff.
You could just disguise the games to look like games that are existing on eshop. For example, playing rom hacks, just inject the rom, and keep the picture and other data untouched so it looks like Super mario world, but is really Brutal Mario world. Mega Man 4 is actually Rockman 4 minus infinity. Is not supicious now cause it still has the normal picture and name and everything of the eshop download but is only you know the game is injected.