If you jailbreak your iPhone, it will work exactly how it does, appstore doesn't change, although you can then get free apps from install0us (google it).
The only thing is that you CANNOT just update your phone with iTunes. You will have to wait for the "dev-team" (<-- the people behind the jailbreak) to release a new jailbreak and/or jailbreak tool. But that never takes too long. Firmware 4.0 has been jailbroken for quite some time and isn't even released to the public until later this week.
I would highly recommend the jailbreak and I wouldn't own an iPhone without it.
good luck!