1. Apps are sorta on both if you are using a custom rom, otherwise they are in internal memory not on the SD card. You can delete them with astro on the phone itself, but its safer to do it through the SDK (shell).
2. Yes, you can delete all the rooting stuff, but copy it to ur pc 1st just in case you need it. I managed to unroot mine few times accidentally and had to go scrounging because i deleted them.