1. Will I still get the apple software updates through iTunes when they release them?
NEVER update with an apple firmware update UNLESS you understand the consequences.
It will RE-LOCK your phone if it is unlocked.
It will REMOVE THE JAILBREAK and ALL THIRD PARTY APPs.
If Apple are sneaky they may purposely break your iPhone with an update as they did with the 1.1.1 update but which the DevTeam fixed.
PwnageTool DOES work with 2.0 Beta versions and it will be updated when the official firmware is out so you will be able to update and keep your unlock and/or jailbreak and 3rd party apps.
2. Can I still download anything I want from iTunes or any SDK apps I want?
You can use iTunes music/movie/tv downloads as normal - that doesn't change.
We don't know how the SDK apps will work yet but I would imagine the answer is yes. IF there are any problems between a jailbreaked phone and the iTunes AppStore then the DevTeam *who hack the iphone* will fix it as quickly as possible.
3. Please let me know any known disadvantages that I might have if I jailbreak or unlock my iPhone.
If you use pwnage to unlock/jailbreak your phone it is 100% reversible.
You can relock using BootNeuter (the unlocking application that runs on the phone).
And remove all signs of jailbreaking by restoring to official iPhone firmware and setting the phone up as a new phone - not from a backup and then activating using iTunes officially.
Of course if your not going to be on AT&T then Apple won't give you a warranty anyway as your not contracted with the phone network so it doesn't matter!