So quick overview of the game. It's structured like Kurasuke's previous game, Night Tail/Nightmare Hunter, with a main story and erotic sidestories. The H-scenes are mostly concentrated in the defeat scenes in the main story and the erotic sidestories, of which there are 7. Four of them (Nao's predicament, Mushroom Kingdom, Occult Club, and Hypnosis) focus on Arisa, Rika and Stella get one each, and a final sidestory featuring all three. The main story is composed of IIRC 5 chapters and final true epilogue that assumes you've finished all the side stories.
Sorta. The piercings appear in the last quarter of two of the sidestories and thus appear mostly in 3-4 h-scenes. Once you have finished the sidestory though, you can buy the costumes featured in that sidestory as cosmetic equipment. There's also post-game (non-canon) extensions of the bad ends which feature the piercings a lot more.
Depends on the scenario, but it ranges from common sense or values alteration, to false memories, to outright personality replacement. Most of the side stories have some form of mind control, but aside from the Hypnosis and Mushroom Kingdom stories, it's pretty subtle.