1.) Rooting doesn't lose features...installing a development rom will (Froyo atm) because it's still in development. But rooting is merely gaining access to the locked portions of your phone so it should not have any effect on features (though does affect how much you can damage if you don't understand things fully).
2.) Again, this only applies to installing a ROM and it's an exercise in trust. Is there a way to hide things from the majority? sure...with a wide base of users who are somewhat tech-savvy, it's harder but it could still be done. Ultimately, it comes down to whether or not you trust them...in the same way it comes down to whether or not you trust HTC for the exact same thing (they could hide info gathering tools too if they wanted).
The risk is there but unlikely with anything that sticks around a while...if you're worried about such things and want the most stable comfortable experience...stick with stock (at least for a while) until things have settled on the forums into a groove where you have the main few devs who have built a good reputation for themselves. (Toast and Flipz have built a good reputation for themselves on the CDMA Hero forums already but ultimately, it's you who have to decide who you want to trust. If you're truely paranoid, you could even add the concern that I'm just a propaganda spreading sleaze trying to allay your worries to get you to root and take over your phone, etc).
You can see, it can become a slippery slope if you overthink things. My suggestion is to watch and keep tabs on things going on...not only will you learn a lot about the whole process but you'll start seeing the non-tangible things that tell you where you can put your trust...or evidence that you should stay stock for a while longer.
Sprint EVO (Fresh latest w/Netarchy-toastmod-4.2 cfs-bfq-havs-more-smartass-universal-signed)