Is removing the entire end cap off of my exhaust going to result in decreased performance. I already have many mods done to the bike and also have rejetted it...thanks

Removing the whole end cap will only make your bike loud. you need to have a little more back presure.
Do a search for the baffle mod.

So really there's no Performance loss? I've seen other people do it...currently I only have the end cap with no spark arrestor

Loud does not mean fast. Loud is just annoying and destructive to our right to ride. The reduction in back pressure would actually hurt your bottom end responsiveness.

So, while loosing the bottom end responsiveness and low end torque, do you gain any on top with the free flowing exhaust, or do you just mainly gain noise?  It would seem you would gain something up top.  I currently have my crf230 exhaust stock and it seems like there is plenty of back pressure.

If your exhaust is bone stock with baffle still installed it has way too much backpressure. You also have to consider head pipe size in the backpressure equation. The stock head pipe will only flow as much as it can flow. So opening up the part past that to an excess just makes more noise and also reduces the natural scavenging ability of the exhaust. These bikes are designed to be tractors not top fuel dragsters. Aftermarket exhaust systems have a larger head pipe thus changing the flow charateristics of the entire situation.